Variant report

Variant	rs2296262
Chromosome Location	chr9:117265406-117265407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:117264990..117269271-chr9:117348762..117354798,9	MCF-7	breast:
2	chr9:117159319..117161244-chr9:117264260..117266190,2	MCF-7	breast:
3	chr9:117263907..117271703-chr9:117371218..117376768,10	MCF-7	breast:
4	chr9:117264854..117270088-chr9:117348300..117353117,7	K562	blood:
5	chr9:117262731..117268447-chr9:117369704..117378306,14	K562	blood:
6	chr9:117263501..117265677-chr9:117266069..117268440,2	K562	blood:
7	chr9:117251818..117256354-chr9:117261161..117269778,10	MCF-7	breast:
8	chr9:117263014..117265983-chr9:117266031..117267744,5	MCF-7	breast:
9	chr9:117264226..117271307-chr9:117346303..117355535,28	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000201749	Chromatin interaction
ENSG00000157693	Chromatin interaction
ENSG00000095397	Chromatin interaction
ENSG00000235119	Chromatin interaction
ENSG00000271214	Chromatin interaction
ENSG00000136888	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10759714	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10817628	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[EUR][1000 genomes]
rs10817629	0.97[EUR][1000 genomes]
rs10817631	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10817632	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982238	0.85[TSI][hapmap]
rs10982244	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1324631	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1535964	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1535965	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297814	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527950	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62555200	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478086	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2296262	DFNB31	cis	cerebellum	SCAN
rs2296262	DFNB31	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117240000-117266600	Weak transcription	Gastric	stomach
2	chr9:117245000-117266600	Weak transcription	Right Atrium	heart
3	chr9:117247600-117266400	Weak transcription	Esophagus	oesophagus
4	chr9:117254200-117266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:117259800-117267200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:117260200-117265600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:117260400-117265800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:117263000-117266000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:117263200-117266400	Weak transcription	Spleen	Spleen
10	chr9:117263600-117267000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:117263600-117268400	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr9:117263800-117266800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:117263800-117267000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:117264000-117265800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr9:117264000-117265800	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr9:117264000-117266400	Enhancers	Fetal Intestine Large	intestine
17	chr9:117264000-117266400	Flanking Active TSS	Hela-S3	cervix
18	chr9:117264000-117266800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:117264200-117265600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr9:117264200-117265800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:117264200-117265800	Enhancers	Pancreas	Pancrea
22	chr9:117264200-117266200	Enhancers	Fetal Lung	lung
23	chr9:117264200-117266600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:117264200-117266600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr9:117264200-117268200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:117264200-117268400	Active TSS	Brain Angular Gyrus	brain
27	chr9:117264400-117265600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:117264400-117265600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:117264400-117265600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:117264400-117266000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr9:117264400-117266400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:117264400-117266400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:117264400-117266400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:117264400-117266600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr9:117264400-117266800	Flanking Active TSS	K562	blood
36	chr9:117264600-117265600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr9:117264600-117265600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr9:117264600-117265800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:117264600-117265800	Weak transcription	Fetal Kidney	kidney
40	chr9:117264600-117266000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr9:117264600-117266000	Enhancers	Adipose Nuclei	Adipose
42	chr9:117264600-117266000	Enhancers	Fetal Intestine Small	intestine
43	chr9:117264600-117266000	Enhancers	NHEK	skin
44	chr9:117264600-117266200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr9:117264600-117266200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:117264600-117266400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:117264600-117266600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:117264600-117268200	Active TSS	Brain Cingulate Gyrus	brain
49	chr9:117264600-117268400	Active TSS	Brain Substantia Nigra	brain
50	chr9:117264600-117268600	Active TSS	Pancreatic Islets	Pancreatic Islet

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