Variant report

Variant	rs334533
Chromosome Location	chr3:119792882-119792883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119792020..119796349-chr3:119811485..119815699,5	K562	blood:
2	chr3:119790138..119793520-chr3:119812637..119815168,3	K562	blood:
3	chr3:119791224..119794073-chr3:119813064..119815641,4	MCF-7	breast:
4	chr3:119786174..119787681-chr3:119792376..119794178,2	MCF-7	breast:
5	chr3:119790797..119794267-chr3:119811448..119815142,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11915717	0.83[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.87[JPT][hapmap]
rs12630592	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]
rs12634476	0.87[JPT][hapmap]
rs12634889	0.86[JPT][hapmap]
rs12638973	0.85[JPT][hapmap]
rs13314595	0.82[CEU][hapmap]
rs13321783	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[ASN][1000 genomes]
rs1574154	0.87[JPT][hapmap]
rs1579031	0.82[CEU][hapmap]
rs16830689	0.82[CEU][hapmap]
rs1719890	0.81[ASN][1000 genomes]
rs1719894	0.81[ASN][1000 genomes]
rs17204878	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1732168	0.81[ASN][1000 genomes]
rs1732170	0.81[ASN][1000 genomes]
rs17810676	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2126583	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2199503	0.91[JPT][hapmap]
rs2319398	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];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs2319399	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs28536662	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334535	0.82[CEU][hapmap]
rs334536	0.82[CEU][hapmap]
rs334553	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334559	0.82[CEU][hapmap]
rs334563	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs334564	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs334566	0.81[CEU][hapmap]
rs4072520	0.82[CEU][hapmap]
rs4340737	0.87[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687892	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687893	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688046	0.87[JPT][hapmap]
rs4688047	0.87[JPT][hapmap]
rs4688054	0.87[JPT][hapmap]
rs4688059	0.81[JPT][hapmap]
rs57695730	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58605236	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6438555	0.82[CEU][hapmap]
rs6769435	0.82[CEU][hapmap]
rs6770314	0.82[CEU][hapmap]
rs6771023	0.82[CEU][hapmap]
rs6779828	0.82[CEU][hapmap]
rs6781942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6792572	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];1.00[MKK][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs6795653	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];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[ASN][1000 genomes]
rs6796420	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800622	0.81[ASN][1000 genomes]
rs6808975	0.82[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7617372	0.81[CEU][hapmap]
rs7620750	0.86[CEU][hapmap]
rs7624540	0.82[CEU][hapmap]
rs7639388	0.91[JPT][hapmap]
rs7641045	0.81[ASN][1000 genomes]
rs7643875	0.83[EUR][1000 genomes]
rs7644234	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652172	0.82[CEU][hapmap]
rs968824	0.82[CEU][hapmap]
rs9813864	0.81[ASN][1000 genomes]
rs9851174	0.82[CEU][hapmap]
rs9859778	0.82[CEU][hapmap]
rs9866394	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873477	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];1.00[MKK][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs9878473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs9879295	0.83[ASN][1000 genomes]
rs9879992	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs334533	GSK3B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119760200-119805400	Weak transcription	HMEC	breast
2	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:119771800-119805400	Weak transcription	NHEK	skin
6	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
7	chr3:119775800-119796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:119775800-119797600	Weak transcription	Fetal Thymus	thymus
9	chr3:119778800-119796000	Weak transcription	NHDF-Ad	bronchial
10	chr3:119778800-119796400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:119779400-119804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:119779400-119807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:119779600-119793000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:119779600-119800200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:119779600-119807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:119779800-119793000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:119780600-119807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:119784400-119796400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:119784400-119797200	Weak transcription	Thymus	Thymus
20	chr3:119785400-119796800	Weak transcription	Dnd41	blood
21	chr3:119786600-119794800	Weak transcription	Hela-S3	cervix
22	chr3:119786600-119796000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:119786600-119797600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:119788000-119793000	Weak transcription	GM12878-XiMat	blood
25	chr3:119788400-119795800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:119788400-119796200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:119788400-119805400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:119788400-119808600	Weak transcription	Primary B cells from cord blood	blood
29	chr3:119789400-119797000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:119789400-119809200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:119789800-119797200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:119789800-119807800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr3:119790000-119793800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:119790000-119797800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:119790000-119807600	Weak transcription	Liver	Liver
36	chr3:119790200-119796000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:119790200-119805000	Weak transcription	HepG2	liver
38	chr3:119790400-119794800	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:119790400-119796000	Weak transcription	Fetal Lung	lung
40	chr3:119790400-119800000	Weak transcription	Spleen	Spleen
41	chr3:119790400-119800600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:119790400-119805200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:119790600-119796000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:119790600-119797200	Weak transcription	Primary T cells from cord blood	blood
45	chr3:119790600-119797600	Weak transcription	Right Atrium	heart
46	chr3:119790600-119797800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:119790600-119807400	Weak transcription	Brain Substantia Nigra	brain
48	chr3:119790600-119807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:119790600-119809200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:119790800-119794600	Weak transcription	Small Intestine	intestine

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