Variant report

Variant	rs12630592
Chromosome Location	chr3:119768246-119768247
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119766647..119769158-chr3:119813625..119815410,2	K562	blood:
2	chr3:119766726..119769523-chr3:119811543..119814551,3	MCF-7	breast:
3	chr3:119766444..119768351-chr3:119810376..119812777,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10433404	0.87[JPT][hapmap]
rs10934502	0.87[JPT][hapmap]
rs10934503	0.86[JPT][hapmap]
rs10934505	0.87[JPT][hapmap]
rs10934506	0.87[JPT][hapmap]
rs10934507	0.85[JPT][hapmap]
rs1154595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11915717	0.83[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12634476	0.87[JPT][hapmap]
rs12634889	0.86[JPT][hapmap]
rs12638973	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs13321783	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.84[ASN][1000 genomes]
rs1574154	0.87[JPT][hapmap]
rs1719890	0.82[ASN][1000 genomes]
rs1719891	0.81[ASN][1000 genomes]
rs1719894	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs17204878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1732168	0.82[ASN][1000 genomes]
rs1732170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs17810676	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870931	0.87[JPT][hapmap]
rs1903765	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2126583	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2199503	0.91[JPT][hapmap]
rs2319398	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs2319399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs28536662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3107669	0.81[ASN][1000 genomes]
rs334533	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334553	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334564	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4340737	0.87[JPT][hapmap]
rs4491945	0.81[ASN][1000 genomes]
rs4624596	0.87[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687892	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688042	0.87[JPT][hapmap]
rs4688046	0.87[JPT][hapmap]
rs4688047	0.87[JPT][hapmap]
rs4688054	0.87[JPT][hapmap]
rs4688059	0.81[JPT][hapmap]
rs57695730	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58605236	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6438552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6781942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6792572	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs6795653	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs6796420	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs6808975	0.83[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7620750	0.82[CEU][hapmap]
rs7633279	0.87[JPT][hapmap]
rs7639388	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7641045	0.82[ASN][1000 genomes]
rs7643875	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7644234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs9866394	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[ASN][1000 genomes]
rs9878473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs9879295	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12630592	GSK3B	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119757800-119769800	ZNF genes & repeats	Dnd41	blood
2	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
3	chr3:119760000-119770200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:119760000-119771200	Weak transcription	NHDF-Ad	bronchial
5	chr3:119760200-119768600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:119760200-119768800	Weak transcription	Ovary	ovary
7	chr3:119760200-119779400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:119760200-119805400	Weak transcription	HMEC	breast
9	chr3:119761200-119769200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:119763200-119769600	Weak transcription	Gastric	stomach
11	chr3:119764400-119769800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:119764600-119768800	Weak transcription	Aorta	Aorta
13	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:119764800-119769400	Weak transcription	Fetal Lung	lung
15	chr3:119765000-119768400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:119765000-119769000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:119765000-119770800	Weak transcription	Primary B cells from cord blood	blood
18	chr3:119765200-119768400	Weak transcription	Fetal Brain Female	brain
19	chr3:119765200-119771200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:119765600-119769400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:119766200-119771800	Enhancers	Colon Smooth Muscle	Colon
22	chr3:119766400-119769000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:119766400-119769200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:119766400-119769200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:119766400-119769400	Weak transcription	NHEK	skin
26	chr3:119766400-119772200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:119766400-119772600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:119766600-119771400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:119766600-119771800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:119766800-119768600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:119766800-119769000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:119766800-119769200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:119766800-119770000	Enhancers	Brain Angular Gyrus	brain
34	chr3:119767000-119770400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:119767200-119769600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:119767200-119771600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr3:119767200-119771800	Enhancers	Primary T cells from cord blood	blood
38	chr3:119767400-119768600	Weak transcription	Psoas Muscle	Psoas
39	chr3:119767400-119768600	Weak transcription	Right Atrium	heart
40	chr3:119767400-119768600	Weak transcription	Small Intestine	intestine
41	chr3:119767400-119768800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:119767400-119769800	Enhancers	Brain Substantia Nigra	brain
43	chr3:119767400-119770000	Enhancers	Right Ventricle	heart
44	chr3:119767400-119770400	Enhancers	Brain Anterior Caudate	brain
45	chr3:119767400-119771200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:119767400-119771400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:119767400-119771800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr3:119767400-119772400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:119767600-119769000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:119767600-119769200	Weak transcription	Rectal Smooth Muscle	rectum

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