Variant report

Variant	rs10939862
Chromosome Location	chr5:60001644-60001645
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:59998583..60001649-chr5:60008376..60010857,3	K562	blood:
2	chr5:59994459..59997012-chr5:59999943..60002207,3	K562	blood:
3	chr5:59996423..59998684-chr5:60001090..60003995,3	MCF-7	breast:
4	chr5:59994459..59997087-chr5:60000577..60002875,2	K562	blood:

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10043291	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10050803	0.88[CEU][hapmap]
rs10054744	0.83[ASN][1000 genomes]
rs10058456	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10069929	0.83[ASN][1000 genomes]
rs10440618	0.83[ASN][1000 genomes]
rs10471493	0.82[ASN][1000 genomes]
rs10805370	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10939858	0.90[ASN][1000 genomes]
rs10939860	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117674	0.82[ASN][1000 genomes]
rs1117675	0.83[ASN][1000 genomes]
rs1117677	0.83[ASN][1000 genomes]
rs11739724	0.81[EUR][1000 genomes]
rs11740327	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs11741754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11745627	0.82[EUR][1000 genomes]
rs11948543	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs11952735	0.83[EUR][1000 genomes]
rs11954496	0.84[ASN][1000 genomes]
rs11955398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11956023	0.88[EUR][1000 genomes]
rs11959922	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs12186391	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514253	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12515025	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517174	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12517207	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12522801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651791	0.82[ASN][1000 genomes]
rs12655515	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12655977	0.83[ASN][1000 genomes]
rs1379114	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1379115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1379116	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379117	0.85[EUR][1000 genomes]
rs1444237	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs1456742	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1456743	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1460958	0.84[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1562235	0.83[EUR][1000 genomes]
rs17387940	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1816899	0.82[EUR][1000 genomes]
rs1824120	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870014	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1960479	0.83[ASN][1000 genomes]
rs1992612	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2045356	0.85[CEU][hapmap]
rs2061250	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs206789	0.82[CHD][hapmap]
rs2085409	0.88[ASN][1000 genomes]
rs2085410	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2085411	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2085413	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2100584	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2409792	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409794	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs286153	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs286154	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs286158	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2898287	0.82[EUR][1000 genomes]
rs2898288	0.88[ASN][1000 genomes]
rs3857236	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs3899221	0.83[ASN][1000 genomes]
rs4277863	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4398599	0.83[ASN][1000 genomes]
rs4400080	0.83[ASN][1000 genomes]
rs4406099	0.81[ASN][1000 genomes]
rs4447941	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4524466	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4577661	0.83[ASN][1000 genomes]
rs4700380	0.84[EUR][1000 genomes]
rs4700384	0.83[ASN][1000 genomes]
rs4700388	0.81[ASN][1000 genomes]
rs55720622	0.83[EUR][1000 genomes]
rs55854817	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56191602	0.86[EUR][1000 genomes]
rs56726435	0.97[ASN][1000 genomes]
rs57521726	0.81[EUR][1000 genomes]
rs62373024	0.83[EUR][1000 genomes]
rs62373025	0.82[EUR][1000 genomes]
rs6449483	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6449485	0.81[EUR][1000 genomes]
rs6449487	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6449490	0.84[ASN][1000 genomes]
rs6449491	0.84[ASN][1000 genomes]
rs6449493	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs6874072	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6882727	0.84[ASN][1000 genomes]
rs6887434	0.83[ASN][1000 genomes]
rs6887637	0.81[ASN][1000 genomes]
rs755077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701708	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7707698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709056	0.81[ASN][1000 genomes]
rs7719726	0.89[TSI][hapmap]
rs7720233	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs7730342	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7736518	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs897672	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs930864	0.87[ASN][1000 genomes]
rs9654363	0.83[ASN][1000 genomes]
rs9686489	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9942410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv1794154	chr5:59995393-60012235	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1821070	chr5:59995393-60012235	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1801919	chr5:59995393-60013913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
12	esv3468468	chr5:59999795-60005493	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv3399648	chr5:60000595-60004743	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv3468470	chr5:60000720-60004968	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv3443840	chr5:60000970-60004693	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv513242	chr5:60001088-60003691	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv2441489	chr5:60001180-60004589	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv3468473	chr5:60001223-60004020	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv3468466	chr5:60001495-60004193	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv1924343	chr5:60001528-60003856	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv821130	chr5:60001557-60003847	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv823083	chr5:60001557-60003847	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv823084	chr5:60001579-60003195	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv823085	chr5:60001579-60003263	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv1009755	chr5:60001579-60003470	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv823086	chr5:60001579-60003470	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	esv3468472	chr5:60001583-60003772	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	esv3501854	chr5:60001601-60003780	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	esv3501859	chr5:60001604-60003747	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	esv3501856	chr5:60001623-60003702	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv3468475	chr5:60001631-60003738	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	esv3468471	chr5:60001636-60003736	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	esv3468469	chr5:60001643-60003693	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10939862	ERCC8	cis	multi-tissue	Pritchard

Chromatin state (count:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59996800-60001800	Enhancers	Placenta	Placenta

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