Variant report

Variant	rs225660
Chromosome Location	chr6:142488512-142488513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:142488287-142488604	ProgFib	skin:	n/a	n/a

Variant related genes	Relation type
VTA1	TF binding region

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[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.97[ASN][1000 genomes]
rs225601	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225602	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225604	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs225605	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs225606	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225618	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225620	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs225622	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225623	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225624	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225628	0.90[EUR][1000 genomes]
rs225629	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225630	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225632	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[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];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225633	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225634	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225635	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225636	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225637	0.91[EUR][1000 genomes]
rs225639	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225640	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225641	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225643	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225650	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225651	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225654	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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225655	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225656	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225657	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225661	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225664	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225667	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225668	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225670	1.00[ASN][1000 genomes]
rs225671	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]
rs225672	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225673	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs225675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs225676	1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[ASN][1000 genomes]
rs225677	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs225678	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs225679	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs225680	0.97[ASN][1000 genomes]
rs225682	0.97[ASN][1000 genomes]
rs225683	0.97[ASN][1000 genomes]
rs225684	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs225685	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs225686	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs225687	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs225688	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225689	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs225690	0.97[ASN][1000 genomes]
rs225692	0.97[ASN][1000 genomes]
rs225693	0.97[ASN][1000 genomes]
rs225695	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs225696	0.97[ASN][1000 genomes]
rs225697	0.97[ASN][1000 genomes]
rs225698	0.97[ASN][1000 genomes]
rs225700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs225701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs225702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs225704	0.97[ASN][1000 genomes]
rs225705	0.97[ASN][1000 genomes]
rs225706	0.97[ASN][1000 genomes]
rs225707	0.97[ASN][1000 genomes]
rs225708	0.97[ASN][1000 genomes]
rs225709	0.96[ASN][1000 genomes]
rs225710	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[ASN][1000 genomes]
rs225728	0.83[ASN][1000 genomes]
rs4896574	0.84[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4896575	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs56185739	1.00[ASN][1000 genomes]
rs62430473	0.93[ASN][1000 genomes]
rs62430506	0.85[ASN][1000 genomes]
rs628311	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638804	0.90[ASN][1000 genomes]
rs639658	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];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
rs225660	VTA1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
2	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
3	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
4	chr6:142474600-142500800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
6	chr6:142477200-142500600	Weak transcription	Fetal Brain Male	brain
7	chr6:142477400-142488600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:142477600-142499600	Weak transcription	Stomach Mucosa	stomach
9	chr6:142477800-142491800	Weak transcription	NHLF	lung
10	chr6:142479400-142491800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:142481400-142494400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:142481600-142497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:142481800-142488600	Weak transcription	Pancreas	Pancrea
14	chr6:142481800-142495000	Weak transcription	Gastric	stomach
15	chr6:142483200-142499800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:142484000-142488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:142484200-142488600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
19	chr6:142484400-142491800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:142484400-142494400	Weak transcription	Fetal Lung	lung
21	chr6:142484400-142498400	Weak transcription	Psoas Muscle	Psoas
22	chr6:142484600-142491000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:142484600-142493400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:142484600-142494400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:142484600-142510000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:142486400-142495000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:142486400-142497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:142486600-142493600	Weak transcription	Fetal Kidney	kidney
29	chr6:142486600-142494400	Weak transcription	HMEC	breast
30	chr6:142486600-142498000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:142486800-142488600	Weak transcription	Fetal Heart	heart
32	chr6:142486800-142492800	Weak transcription	Brain Substantia Nigra	brain
33	chr6:142486800-142496200	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:142486800-142497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:142487000-142489600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:142487000-142496200	Strong transcription	Fetal Thymus	thymus
37	chr6:142487200-142489200	Strong transcription	Dnd41	blood
38	chr6:142487200-142498000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:142487400-142489000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:142487400-142489200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:142487400-142489400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:142487400-142489400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:142487400-142489400	Strong transcription	HepG2	liver
44	chr6:142487400-142489600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:142487400-142495600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:142487400-142495800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:142487400-142496200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:142487400-142497000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:142487400-142498400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:142487400-142499000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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