Variant report

Variant	rs9657665
Chromosome Location	chr9:117232351-117232352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117160026..117162486-chr9:117230944..117233516,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235119	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513247	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10733610	0.82[CEU][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10739413	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739414	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739415	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10759707	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10817611	0.86[JPT][hapmap]
rs10817613	0.80[EUR][1000 genomes]
rs10817614	0.91[JPT][hapmap]
rs10817615	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10817616	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817617	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10817618	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982222	0.91[CEU][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10982225	0.82[ASN][1000 genomes]
rs10982229	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982235	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1324630	0.81[LWK][hapmap]
rs1324633	1.00[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1324634	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1324635	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1408528	0.81[LWK][hapmap]
rs2147436	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4304391	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4978590	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4979393	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4979394	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4979397	0.81[LWK][hapmap]
rs4979399	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4979402	0.81[LWK][hapmap]
rs4979407	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4979408	0.86[ASN][1000 genomes]
rs7044404	0.90[ASN][1000 genomes]
rs718841	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs72750719	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7852132	0.91[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9657662	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9657663	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9657664	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9657666	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
5	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases
6	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv615235	chr9:116958144-117367061	ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
19	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
20	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
22	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
23	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
24	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
25	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
26	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
28	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
29	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
30	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
31	nsv1050256	chr9:117106276-117247033	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
32	nsv540206	chr9:117106276-117247033	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
33	nsv831693	chr9:117116450-117281895	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9657665	C9orf80	cis	parietal	SCAN
rs9657665	DFNB31	cis	parietal	SCAN
rs9657665	SNORA70C	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117203000-117237800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:117216600-117234800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:117217800-117242600	Weak transcription	HepG2	liver
4	chr9:117220400-117246600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:117222000-117238800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:117222200-117244600	Weak transcription	K562	blood
7	chr9:117222600-117246800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:117223200-117239200	Weak transcription	Fetal Intestine Large	intestine
9	chr9:117223400-117233600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:117223800-117237000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:117224000-117238600	Weak transcription	Brain Angular Gyrus	brain
12	chr9:117225000-117239400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:117225400-117239000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:117225600-117245800	Weak transcription	Fetal Lung	lung
15	chr9:117226400-117242600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:117227800-117247000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:117228800-117232600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:117228800-117237800	Weak transcription	Thymus	Thymus
19	chr9:117229800-117232400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:117230200-117234200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:117230400-117238600	Weak transcription	Gastric	stomach
22	chr9:117230600-117232600	Weak transcription	Pancreas	Pancrea
23	chr9:117230600-117234000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:117230800-117232400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:117230800-117234400	Weak transcription	Esophagus	oesophagus
26	chr9:117231000-117233000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:117231000-117233600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:117231200-117232400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:117231200-117232800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:117231400-117234200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:117231600-117232400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr9:117231600-117239000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:117231600-117240600	Strong transcription	Brain Substantia Nigra	brain
34	chr9:117231800-117232600	Strong transcription	Brain Hippocampus Middle	brain
35	chr9:117231800-117232800	ZNF genes & repeats	Ovary	ovary
36	chr9:117231800-117233000	ZNF genes & repeats	Fetal Stomach	stomach
37	chr9:117232000-117232400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr9:117232000-117232400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:117232000-117232400	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr9:117232000-117232600	ZNF genes & repeats	Spleen	Spleen
41	chr9:117232000-117233000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:117232200-117232400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
43	chr9:117232200-117232400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
44	chr9:117232200-117235000	Weak transcription	Brain Anterior Caudate	brain

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