Variant report

Variant	rs6795653
Chromosome Location	chr3:119610565-119610566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119610347..119611160-chr3:119865685..119866515,3	MCF-7	breast:
2	chr3:119609509..119613184-chr3:119810237..119814414,6	MCF-7	breast:
3	chr3:119609229..119612218-chr3:119810984..119813598,2	K562	blood:
4	chr3:119605247..119607921-chr3:119609001..119610890,2	MCF-7	breast:
5	chr3:119610502..119611380-chr3:119901494..119902513,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10433404	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934500	0.87[JPT][hapmap]
rs10934502	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934503	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10934505	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934506	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10934507	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1154595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11915717	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11921360	0.91[JPT][hapmap]
rs12629015	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs12630592	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]
rs12634476	0.87[JPT][hapmap]
rs12634889	0.86[JPT][hapmap]
rs12638973	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs13321783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546753	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1574154	0.87[JPT][hapmap]
rs1719890	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719891	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719894	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17204878	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[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs1732168	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1732170	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17810676	0.82[ASN][1000 genomes]
rs1870931	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1903765	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs2126583	0.84[ASN][1000 genomes]
rs2199503	0.91[JPT][hapmap]
rs2319398	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2319399	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[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2472682	0.91[CEU][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs28536662	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[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2873950	0.82[JPT][hapmap]
rs3107669	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334533	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]
rs334553	0.82[ASN][1000 genomes]
rs334563	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]
rs3732359	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3732360	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3732361	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4261913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4340737	0.87[JPT][hapmap]
rs4491945	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4624596	0.87[JPT][hapmap]
rs4687890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4687892	0.83[ASN][1000 genomes]
rs4687893	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4688042	0.87[JPT][hapmap]
rs4688046	0.87[JPT][hapmap]
rs4688047	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4688054	0.87[JPT][hapmap]
rs57695730	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58605236	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438552	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6785049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6792572	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796420	0.85[ASN][1000 genomes]
rs6800622	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6805251	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]
rs6808874	0.87[JPT][hapmap]
rs6808975	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7431209	0.95[JPT][hapmap]
rs7611736	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7620750	0.82[CEU][hapmap]
rs7633279	0.87[JPT][hapmap]
rs7639388	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7641045	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643875	0.80[AMR][1000 genomes]
rs7644234	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[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9813864	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866394	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9873477	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878473	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879295	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6795653	MUC13	cis	parietal	SCAN
rs6795653	GSK3B	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
3	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
4	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:119582400-119610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:119582400-119610600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
11	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
12	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
13	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:119582600-119610600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:119582600-119611000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:119582600-119611000	Weak transcription	NHLF	lung
17	chr3:119582600-119627200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
19	chr3:119582800-119621200	Weak transcription	Fetal Intestine Large	intestine
20	chr3:119583000-119611000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:119583600-119621400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:119584000-119622800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:119592600-119617800	Weak transcription	Osteobl	bone
25	chr3:119594800-119610800	Weak transcription	Stomach Mucosa	stomach
26	chr3:119597600-119659000	Weak transcription	Gastric	stomach
27	chr3:119599800-119611000	Weak transcription	Fetal Kidney	kidney
28	chr3:119599800-119611000	Weak transcription	NH-A	brain
29	chr3:119600000-119610800	Weak transcription	Fetal Brain Male	brain
30	chr3:119600000-119611000	Weak transcription	Adipose Nuclei	Adipose
31	chr3:119601000-119610600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:119601000-119611000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:119603200-119610600	Weak transcription	HSMM	muscle
34	chr3:119603200-119611000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:119603200-119611000	Weak transcription	HMEC	breast
36	chr3:119603400-119611000	Weak transcription	HSMMtube	muscle
37	chr3:119603400-119614600	Weak transcription	NHEK	skin
38	chr3:119603400-119624200	Weak transcription	Hela-S3	cervix
39	chr3:119603600-119624200	Weak transcription	HepG2	liver
40	chr3:119604800-119627800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:119607000-119611000	Weak transcription	A549	lung
42	chr3:119608000-119611000	Weak transcription	Aorta	Aorta
43	chr3:119608000-119621600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:119608000-119627800	Weak transcription	Left Ventricle	heart
45	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:119608200-119610600	Weak transcription	Liver	Liver
47	chr3:119608200-119610600	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:119608200-119611000	Weak transcription	Fetal Intestine Small	intestine
49	chr3:119608200-119611000	Weak transcription	Ovary	ovary
50	chr3:119608200-119613800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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