Variant report

Variant	rs6805251
Chromosome Location	chr3:119560606-119560607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119559434..119561964-chr3:119812906..119815374,2	MCF-7	breast:
2	chr3:119553090..119555920-chr3:119558108..119560664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10433404	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10934500	0.86[JPT][hapmap]
rs10934502	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10934503	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1154595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11915717	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12634476	0.86[JPT][hapmap]
rs12634889	0.86[JPT][hapmap]
rs12638973	0.85[JPT][hapmap]
rs13314595	0.81[CEU][hapmap]
rs13321783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1546753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574154	0.86[JPT][hapmap]
rs1579031	0.81[CEU][hapmap]
rs1719889	0.81[CEU][hapmap]
rs1719890	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719891	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719894	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[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732168	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1732170	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1870931	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1903765	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs2037547	0.81[CEU][hapmap]
rs2126583	0.81[ASN][1000 genomes]
rs2319398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2319399	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[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2472682	0.90[CEU][hapmap];0.83[AMR][1000 genomes]
rs28536662	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[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2873950	0.86[JPT][hapmap]
rs3107669	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732359	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3732360	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs3732361	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4072520	0.81[CEU][hapmap]
rs4261913	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4340737	0.86[JPT][hapmap]
rs4491945	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4624596	0.86[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4688042	0.86[JPT][hapmap]
rs4688046	0.86[JPT][hapmap]
rs4688047	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4688054	0.86[JPT][hapmap]
rs57695730	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58605236	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6438552	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769435	0.81[CEU][hapmap]
rs6770314	0.81[CEU][hapmap]
rs6771023	0.81[CEU][hapmap]
rs6781942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790751	0.81[CEU][hapmap]
rs6792572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6796420	0.81[ASN][1000 genomes]
rs6800622	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808874	0.86[JPT][hapmap]
rs6808975	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7617372	0.81[CEU][hapmap]
rs7620750	0.81[CEU][hapmap]
rs7624540	0.81[CEU][hapmap]
rs7633279	0.86[JPT][hapmap]
rs7639388	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7641045	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7644234	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829763	0.81[CEU][hapmap]
rs9851174	0.81[CEU][hapmap]
rs9866394	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9873477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9878473	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879295	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9879992	0.81[CEU][hapmap]

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	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	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

Variant related diseases (count:1)

Disease	PMID	Source
HDL cholesterol	24097068	GWAS catalog

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
3	chr3:119536200-119569000	Weak transcription	Esophagus	oesophagus
4	chr3:119536400-119570200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:119536600-119576000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:119536600-119576400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:119539000-119576400	Weak transcription	Ovary	ovary
8	chr3:119540400-119563600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:119540400-119574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:119540400-119576600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:119540800-119577000	Weak transcription	Aorta	Aorta
12	chr3:119541000-119581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:119541200-119561800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:119541200-119587000	Weak transcription	Gastric	stomach
15	chr3:119542400-119581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:119542600-119560800	Weak transcription	Hela-S3	cervix
17	chr3:119542600-119581600	Weak transcription	HUVEC	blood vessel
18	chr3:119542800-119575000	Weak transcription	Fetal Kidney	kidney
19	chr3:119544000-119561800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:119545000-119576400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:119545200-119561600	Weak transcription	Fetal Stomach	stomach
22	chr3:119545200-119562800	Weak transcription	NHLF	lung
23	chr3:119545200-119575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:119545200-119575000	Weak transcription	Adipose Nuclei	Adipose
25	chr3:119545200-119575400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:119545200-119583400	Weak transcription	Brain Angular Gyrus	brain
27	chr3:119545800-119576400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:119545800-119581600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:119546000-119561800	Weak transcription	Left Ventricle	heart
30	chr3:119546000-119561800	Weak transcription	Thymus	Thymus
31	chr3:119546000-119569000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:119546000-119571800	Weak transcription	GM12878-XiMat	blood
33	chr3:119546000-119575000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:119546000-119576400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:119546000-119663400	Weak transcription	Lung	lung
36	chr3:119546200-119561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:119546200-119569000	Weak transcription	Placenta	Placenta
38	chr3:119546200-119575000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:119546400-119567000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:119546400-119575200	Weak transcription	Liver	Liver
41	chr3:119546400-119580400	Weak transcription	HepG2	liver
42	chr3:119548600-119561400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:119548600-119561800	Weak transcription	Primary T cells from cord blood	blood
44	chr3:119548600-119576600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:119548600-119581600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:119548800-119575000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:119549000-119577200	Weak transcription	Small Intestine	intestine
48	chr3:119549200-119574600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:119549200-119581600	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:119549400-119562200	Weak transcription	Fetal Lung	lung

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