Variant report

Variant	rs10957146
Chromosome Location	chr8:61494978-61494979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10091703	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10100740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10101576	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10101714	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10103438	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10109278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110436	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014860	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10435602	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10504311	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap]
rs10957135	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10957136	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10957137	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10957138	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957140	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10957141	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957143	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10957149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774500	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11775407	0.80[EUR][1000 genomes]
rs11778529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778708	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11778772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782178	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782463	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11784284	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11786146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11988528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12678694	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12680436	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12681841	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13266707	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13267765	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13267828	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13269925	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480342	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2326556	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs2326557	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs2625445	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28495747	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28542403	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28678079	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2875966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234629	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34523017	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775344	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35837434	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35853087	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592014	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603239	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610455	0.91[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621279	0.89[CEU][hapmap]
rs624407	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6471884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs649634	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66983460	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669960	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs671275	0.95[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs677467	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684573	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6993237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6995397	0.95[CEU][hapmap]
rs6996344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998294	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7357376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7462738	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812421	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7820349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7822391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7832664	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7832964	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7842105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643524	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530383	chr8:61431756-61605551	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv870164	chr8:61484657-61529482	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv6218	chr8:61485410-61530933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1796952	chr8:61492893-61531418	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10957146	LOC643763	cis	parietal	SCAN
rs10957146	RAB2	cis	lesional skin	skin_eQTL
rs10957146	RAB2	cis	uninvolved skin	skin_eQTL
rs10957146	RAB2A	cis	Heart Left Ventricle	GTEx
rs10957146	RAB2	cis	normal skin	skin_eQTL
rs10957146	RAB2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61448600-61505400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr8:61458200-61497000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:61459400-61495800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr8:61466400-61516800	Weak transcription	Stomach Mucosa	stomach
5	chr8:61467200-61515400	Weak transcription	Fetal Brain Male	brain
6	chr8:61469000-61495000	Weak transcription	Brain Germinal Matrix	brain
7	chr8:61473600-61495000	Weak transcription	Spleen	Spleen
8	chr8:61473600-61497800	Weak transcription	Lung	lung
9	chr8:61474200-61504000	Weak transcription	Colon Smooth Muscle	Colon
10	chr8:61474600-61496200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:61474600-61496400	Weak transcription	Thymus	Thymus
12	chr8:61474800-61496000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr8:61474800-61504000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr8:61475000-61495600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr8:61475400-61498200	Weak transcription	A549	lung
16	chr8:61476200-61495400	Weak transcription	Hela-S3	cervix
17	chr8:61476200-61504800	Weak transcription	NHLF	lung
18	chr8:61476200-61517000	Weak transcription	Brain Angular Gyrus	brain
19	chr8:61476400-61495400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:61476400-61496400	Weak transcription	Brain Substantia Nigra	brain
21	chr8:61476600-61495400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:61476800-61495200	Weak transcription	Brain Anterior Caudate	brain
23	chr8:61477000-61495000	Weak transcription	Ovary	ovary
24	chr8:61477400-61497600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr8:61477800-61496400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr8:61480800-61496600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr8:61481000-61496800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:61481000-61497800	Weak transcription	Gastric	stomach
29	chr8:61481000-61527400	Weak transcription	Psoas Muscle	Psoas
30	chr8:61481200-61504200	Weak transcription	HMEC	breast
31	chr8:61482200-61496200	Weak transcription	Brain Hippocampus Middle	brain
32	chr8:61482800-61496400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr8:61482800-61498000	Weak transcription	Aorta	Aorta
34	chr8:61482800-61504000	Weak transcription	HSMMtube	muscle
35	chr8:61482800-61505800	Weak transcription	Esophagus	oesophagus
36	chr8:61483000-61495000	Weak transcription	Pancreas	Pancrea
37	chr8:61483000-61501200	Weak transcription	NHEK	skin
38	chr8:61483400-61505800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr8:61483600-61496400	Weak transcription	HUVEC	blood vessel
40	chr8:61483800-61515800	Weak transcription	Colonic Mucosa	Colon
41	chr8:61485400-61515400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr8:61485800-61504400	Weak transcription	Small Intestine	intestine
43	chr8:61487000-61495000	Weak transcription	Dnd41	blood
44	chr8:61487000-61497000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr8:61487000-61504800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr8:61487800-61495600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr8:61488800-61496200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr8:61489400-61495000	Weak transcription	HepG2	liver
49	chr8:61489400-61495200	Weak transcription	Left Ventricle	heart
50	chr8:61489400-61495400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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