Variant report

Variant	rs225671
Chromosome Location	chr6:142500925-142500926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11758623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs178783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225601	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225602	0.93[ASN][1000 genomes]
rs225604	0.81[ASW][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs225605	0.87[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs225606	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs225618	0.87[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225620	0.81[ASW][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs225622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225623	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs225624	0.81[ASW][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs225628	0.82[AMR][1000 genomes]
rs225629	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs225630	1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs225631	0.87[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225632	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs225633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225635	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs225636	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225637	0.83[AMR][1000 genomes]
rs225639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225640	0.96[ASN][1000 genomes]
rs225641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225650	1.00[ASN][1000 genomes]
rs225651	1.00[ASN][1000 genomes]
rs225652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs225653	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.99[ASN][1000 genomes]
rs225654	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs225655	1.00[ASN][1000 genomes]
rs225656	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs225657	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs225658	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs225660	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs225661	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs225662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs225663	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225664	1.00[ASN][1000 genomes]
rs225665	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs225666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225667	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225668	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225670	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225672	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225677	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225678	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225680	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225682	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225683	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225688	0.88[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs225689	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225690	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225692	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225693	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225696	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225697	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225698	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225704	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225705	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225706	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225707	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225708	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225709	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225728	0.83[ASN][1000 genomes]
rs4896574	0.90[JPT][hapmap]
rs4896575	0.90[JPT][hapmap]
rs56185739	1.00[ASN][1000 genomes]
rs62430473	0.93[ASN][1000 genomes]
rs62430506	0.85[ASN][1000 genomes]
rs628311	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs638804	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639658	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9389979	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9389980	0.91[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs225671	VTA1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
2	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
3	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
4	chr6:142484600-142510000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:142487800-142502200	Strong transcription	HSMM	muscle
6	chr6:142489000-142543200	Weak transcription	Small Intestine	intestine
7	chr6:142489200-142507400	Weak transcription	Fetal Heart	heart
8	chr6:142492200-142524800	Weak transcription	Brain Angular Gyrus	brain
9	chr6:142495400-142504600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:142495400-142517000	Weak transcription	NHEK	skin
11	chr6:142495600-142510400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:142495600-142513000	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:142495600-142533600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:142495800-142519600	Weak transcription	HMEC	breast
15	chr6:142496000-142525000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:142496000-142528600	Weak transcription	Lung	lung
17	chr6:142496200-142510400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:142496200-142513200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:142496200-142514800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:142496200-142519400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:142496200-142519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:142496200-142527600	Weak transcription	Thymus	Thymus
23	chr6:142496200-142528200	Weak transcription	Fetal Stomach	stomach
24	chr6:142496200-142528400	Weak transcription	Brain Germinal Matrix	brain
25	chr6:142496200-142533800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:142496200-142533800	Weak transcription	Gastric	stomach
27	chr6:142496200-142533800	Weak transcription	Pancreas	Pancrea
28	chr6:142496400-142517200	Weak transcription	Osteobl	bone
29	chr6:142496400-142528000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:142496400-142533600	Weak transcription	Colonic Mucosa	Colon
31	chr6:142496600-142504000	Weak transcription	Right Ventricle	heart
32	chr6:142496600-142505800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:142496600-142519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:142496600-142525800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr6:142496600-142526200	Weak transcription	Esophagus	oesophagus
36	chr6:142496600-142533800	Weak transcription	Left Ventricle	heart
37	chr6:142496600-142546800	Weak transcription	NHLF	lung
38	chr6:142497800-142501600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:142498200-142526000	Weak transcription	Fetal Intestine Small	intestine
40	chr6:142498400-142510200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:142498600-142510000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr6:142498600-142519600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:142498600-142527800	Weak transcription	Ovary	ovary
44	chr6:142498800-142503200	Weak transcription	Fetal Thymus	thymus
45	chr6:142499000-142510400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:142499200-142510600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:142499200-142524800	Weak transcription	HSMMtube	muscle
48	chr6:142499400-142501000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:142499400-142501200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:142499400-142502000	Strong transcription	Primary hematopoietic stem cells	blood

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