Variant report

Variant	rs10939860
Chromosome Location	chr5:59999360-59999361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:59994766..59997434-chr5:59998869..60000673,3	MCF-7	breast:
2	chr5:59984165..59985932-chr5:59998391..60001093,2	K562	blood:
3	chr5:59997848..60001535-chr5:60002216..60006200,5	K562	blood:
4	chr5:59998796..60001597-chr5:60005006..60007976,2	MCF-7	breast:
5	chr5:59998583..60001649-chr5:60008376..60010857,3	K562	blood:
6	chr5:59968561..59971245-chr5:59997935..60000093,2	MCF-7	breast:
7	chr5:59994018..59997409-chr5:59998010..60001591,3	MCF-7	breast:
8	chr5:59998145..60001535-chr5:60003151..60006329,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000035499	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10043291	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10050803	0.88[CEU][hapmap]
rs10054744	0.83[ASN][1000 genomes]
rs10057004	0.81[CEU][hapmap]
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	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10939858	0.90[ASN][1000 genomes]
rs10939862	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];1.00[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];0.83[MEX][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];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs11952735	0.82[EUR][1000 genomes]
rs11954496	0.84[ASN][1000 genomes]
rs11955398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs11956023	0.87[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	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];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]
rs12517174	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs12517207	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs12522801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651791	0.82[ASN][1000 genomes]
rs12655515	0.88[CEU][hapmap];0.80[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1379116	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379117	0.84[EUR][1000 genomes]
rs1444237	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1456742	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[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	0.82[EUR][1000 genomes]
rs17387940	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[ASN][1000 genomes]
rs1816899	0.82[EUR][1000 genomes]
rs1824120	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[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	0.88[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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409794	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs286153	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs286154	0.88[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];1.00[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];0.80[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	0.82[EUR][1000 genomes]
rs55854817	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56191602	0.85[EUR][1000 genomes]
rs56726435	0.97[ASN][1000 genomes]
rs57521726	0.80[EUR][1000 genomes]
rs62373024	0.82[EUR][1000 genomes]
rs62373025	0.81[EUR][1000 genomes]
rs6449483	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs6449485	0.80[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	0.88[CEU][hapmap];0.80[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701708	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7707698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709056	0.81[ASN][1000 genomes]
rs7719726	0.81[CEU][hapmap];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];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7736518	0.96[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	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10939860	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59996800-60001800	Enhancers	Placenta	Placenta
2	chr5:59997000-59999600	Weak transcription	Stomach Mucosa	stomach

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