Variant report

Variant	rs3934600
Chromosome Location	chr9:72002187-72002188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:71996842..72001188-chr9:72001690..72005051,4	MCF-7	breast:
2	chr9:71937269..71941011-chr9:72000572..72004392,4	MCF-7	breast:
3	chr8:128880231..128883034-chr9:72000789..72002321,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10116389	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10746594	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs10746613	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780334	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780344	0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10780360	0.86[JPT][hapmap]
rs10780361	0.86[JPT][hapmap]
rs10867414	0.83[ASN][1000 genomes]
rs10867423	0.82[CEU][hapmap]
rs1334312	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1761290	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1812971	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1929896	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2244720	0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2309431	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2777866	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2777878	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781521	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781522	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781526	0.87[JPT][hapmap]
rs2781527	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3858105	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs3896424	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237232	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4237233	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237234	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4483220	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4484762	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4503164	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4744886	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs4744894	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62570235	0.87[AFR][1000 genomes]
rs6559488	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6559489	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6559490	0.83[ASN][1000 genomes]
rs6559498	0.82[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6559512	0.92[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6559513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6559516	0.87[JPT][hapmap]
rs6559525	0.83[ASN][1000 genomes]
rs6559527	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7019551	0.84[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7033674	0.91[CHD][hapmap];0.87[JPT][hapmap]
rs7043451	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7046199	0.82[CEU][hapmap]
rs7856778	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7866250	0.87[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9314682	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3934600	C9orf57	cis	cerebellum	SCAN
rs3934600	TJP2	cis	parietal	SCAN
rs3934600	TJP2	cis	cerebellum	SCAN
rs3934600	KLF9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
4	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
8	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:71994400-72006800	Weak transcription	Spleen	Spleen
10	chr9:71995000-72012600	Weak transcription	Aorta	Aorta
11	chr9:71996600-72004200	Weak transcription	Right Atrium	heart
12	chr9:71997200-72005000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:71997200-72006600	Weak transcription	HSMMtube	muscle
14	chr9:71997400-72007400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:71997400-72009800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:71997600-72006200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:71997600-72006600	Weak transcription	Fetal Lung	lung
18	chr9:71998200-72005400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr9:71998400-72003600	Strong transcription	Fetal Stomach	stomach
20	chr9:71998600-72003000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:72000000-72005000	Strong transcription	Ovary	ovary
22	chr9:72000200-72003600	Strong transcription	Fetal Muscle Leg	muscle
23	chr9:72000200-72004800	Enhancers	Pancreas	Pancrea
24	chr9:72000200-72005000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr9:72000600-72006600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:72000800-72003200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:72000800-72003400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr9:72001000-72002200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr9:72001000-72002800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:72001000-72003400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:72001000-72006600	Weak transcription	Lung	lung
32	chr9:72001400-72003800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr9:72001600-72002400	Enhancers	Fetal Heart	heart
34	chr9:72001600-72003400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:72001600-72003600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:72001600-72004400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:72001800-72002200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:72001800-72002400	Enhancers	Right Ventricle	heart
39	chr9:72001800-72002600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:72001800-72003200	Genic enhancers	Left Ventricle	heart
41	chr9:72001800-72003400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:72001800-72003400	Strong transcription	Adipose Nuclei	Adipose
43	chr9:72001800-72003400	Strong transcription	Brain Anterior Caudate	brain
44	chr9:72001800-72003400	Enhancers	Psoas Muscle	Psoas
45	chr9:72001800-72006400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:72002000-72002400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr9:72002000-72002400	Strong transcription	Colon Smooth Muscle	Colon
48	chr9:72002000-72002400	Strong transcription	Gastric	stomach
49	chr9:72002000-72003400	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:72002000-72003600	Strong transcription	Fetal Muscle Trunk	muscle

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