Variant report

Variant	rs225657
Chromosome Location	chr6:142487725-142487726
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11758623	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs178783	0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs225601	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225602	0.91[EUR][1000 genomes]
rs225604	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs225605	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs225606	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs225618	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225620	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs225622	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225623	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225624	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225628	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225629	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225630	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225631	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225632	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225633	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225634	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225635	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225636	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225637	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225639	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225640	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225641	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225642	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225643	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225648	0.83[TSI][hapmap]
rs225650	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225651	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225652	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225653	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs225654	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225655	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225656	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225658	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225659	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs225660	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]
rs225661	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs225662	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225663	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225664	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225665	0.92[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225666	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs225667	0.85[ASN][1000 genomes]
rs225668	0.85[ASN][1000 genomes]
rs225670	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs225671	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]
rs225672	0.85[ASN][1000 genomes]
rs225673	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs225674	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225675	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225676	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs225677	1.00[JPT][hapmap]
rs225678	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225679	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225680	0.83[ASN][1000 genomes]
rs225682	0.83[ASN][1000 genomes]
rs225683	0.83[ASN][1000 genomes]
rs225684	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs225685	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225686	0.83[ASN][1000 genomes]
rs225687	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs225689	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225690	0.83[ASN][1000 genomes]
rs225692	0.83[ASN][1000 genomes]
rs225693	0.83[ASN][1000 genomes]
rs225695	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225696	0.83[ASN][1000 genomes]
rs225697	0.83[ASN][1000 genomes]
rs225698	0.83[ASN][1000 genomes]
rs225700	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225701	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs225702	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225704	0.83[ASN][1000 genomes]
rs225705	0.83[ASN][1000 genomes]
rs225706	0.83[ASN][1000 genomes]
rs225707	0.83[ASN][1000 genomes]
rs225708	0.83[ASN][1000 genomes]
rs225709	0.82[ASN][1000 genomes]
rs225710	0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs4896574	0.90[JPT][hapmap]
rs4896575	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs56185739	0.85[ASN][1000 genomes]
rs628311	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs639658	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6939944	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6939975	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.81[JPT][hapmap]
rs9389979	0.81[JPT][hapmap]
rs9389980	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
rs225657	VTA1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142468800-142488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:142469200-142487800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:142469600-142487800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:142469600-142487800	Weak transcription	Thymus	Thymus
5	chr6:142470200-142487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:142470200-142488200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:142470200-142488200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
9	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
10	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
11	chr6:142470800-142487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:142472400-142487800	Weak transcription	Left Ventricle	heart
13	chr6:142472400-142487800	Weak transcription	Ovary	ovary
14	chr6:142472400-142488200	Weak transcription	Primary B cells from cord blood	blood
15	chr6:142473200-142487800	Weak transcription	Lung	lung
16	chr6:142474600-142500800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
18	chr6:142475200-142487800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:142477000-142487800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:142477200-142500600	Weak transcription	Fetal Brain Male	brain
21	chr6:142477400-142487800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:142477400-142487800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:142477400-142487800	Weak transcription	Adipose Nuclei	Adipose
24	chr6:142477400-142487800	Weak transcription	HSMM	muscle
25	chr6:142477400-142488600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:142477600-142487800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:142477600-142488000	Weak transcription	NHDF-Ad	bronchial
28	chr6:142477600-142488000	Weak transcription	NHEK	skin
29	chr6:142477600-142488200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:142477600-142499600	Weak transcription	Stomach Mucosa	stomach
31	chr6:142477800-142487800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:142477800-142488000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:142477800-142491800	Weak transcription	NHLF	lung
34	chr6:142478000-142487800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:142478400-142488000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:142478800-142488000	Weak transcription	GM12878-XiMat	blood
37	chr6:142479400-142491800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:142481400-142494400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:142481600-142497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:142481800-142488200	Weak transcription	Right Ventricle	heart
41	chr6:142481800-142488600	Weak transcription	Pancreas	Pancrea
42	chr6:142481800-142495000	Weak transcription	Gastric	stomach
43	chr6:142483200-142499800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:142484000-142488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:142484200-142488200	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:142484200-142488600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
48	chr6:142484400-142487800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr6:142484400-142488000	Weak transcription	Small Intestine	intestine
50	chr6:142484400-142488400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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