Variant report

Variant	rs2177669
Chromosome Location	chr15:31159169-31159170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10153041	0.93[CHB][hapmap]
rs10163148	0.85[CHB][hapmap]
rs11070624	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070632	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11070678	0.85[CHB][hapmap]
rs11070718	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1133642	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs11631543	0.86[ASN][1000 genomes]
rs11631814	0.93[CHB][hapmap]
rs11638295	0.92[CHB][hapmap]
rs11856544	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12439909	0.83[EUR][1000 genomes]
rs12440244	0.93[CHB][hapmap]
rs12441318	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12441324	0.93[CHB][hapmap]
rs12898883	0.93[CHB][hapmap]
rs12901022	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs12904948	0.93[CHB][hapmap]
rs12904967	0.92[CHB][hapmap]
rs12905321	0.93[CHB][hapmap]
rs12908189	0.93[CHB][hapmap]
rs12911057	0.93[CHB][hapmap]
rs1404468	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs1404469	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1474381	0.85[CHB][hapmap]
rs1474382	0.85[CHB][hapmap]
rs1524876	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1524878	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1809483	0.93[CHB][hapmap]
rs1852034	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880499	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs1880500	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2042613	0.92[CHB][hapmap]
rs2113945	0.85[CHB][hapmap]
rs2113946	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2272218	0.85[CHB][hapmap]
rs2272219	0.85[CHB][hapmap]
rs2293314	0.93[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2293319	0.85[CHB][hapmap]
rs2293320	0.85[CHB][hapmap]
rs2338276	0.93[CHB][hapmap]
rs2339043	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28396629	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28548813	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28693590	0.85[CHB][hapmap]
rs28708881	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28721380	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2873	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs28795529	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2949566	0.86[ASN][1000 genomes]
rs2949569	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2949570	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2949573	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2949575	0.85[CHB][hapmap]
rs2949576	0.85[CHB][hapmap]
rs2949577	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2949578	0.85[CHB][hapmap]
rs2955783	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2955787	0.85[CHB][hapmap]
rs2955790	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs2955791	0.85[CHB][hapmap]
rs2955796	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2955798	0.86[ASN][1000 genomes]
rs2959039	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2959049	0.85[CHB][hapmap]
rs35528291	0.93[CHB][hapmap]
rs3743231	0.85[CHB][hapmap]
rs3829484	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3883068	0.93[CHB][hapmap]
rs4779764	0.93[CHB][hapmap]
rs4779796	0.85[CHB][hapmap]
rs4779797	0.85[CHB][hapmap]
rs56325201	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58844471	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61260387	0.81[EUR][1000 genomes]
rs6493220	0.92[CHB][hapmap]
rs7161812	0.84[CHB][hapmap]
rs7165798	0.92[CHB][hapmap]
rs7169064	0.85[CHB][hapmap]
rs7170710	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs7175951	0.85[CHB][hapmap]
rs7176351	0.85[CHB][hapmap]
rs7178375	0.85[CHB][hapmap]
rs7178533	0.85[CHB][hapmap]
rs7182143	0.92[CHB][hapmap]
rs739831	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs757341	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798088	0.93[CHB][hapmap]
rs798101	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs8023264	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026481	0.93[CHB][hapmap]
rs8040989	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs8041248	0.92[CHB][hapmap]
rs8041717	0.85[CHB][hapmap]
rs8042031	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs811768	0.93[CHB][hapmap]
rs964925	0.90[JPT][hapmap]
rs9806159	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760022	chr15:30292944-31177476	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
2	nsv903757	chr15:30369153-31179534	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1052897	chr15:30501813-31184303	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	esv2757593	chr15:30605836-31177476	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv903822	chr15:30899133-31165955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv1044683	chr15:30954725-31183908	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv542300	chr15:30954725-31183908	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv529701	chr15:30954726-31183907	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
15	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
16	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
17	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
18	nsv903833	chr15:31088443-31174687	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
20	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
21	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
22	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
23	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
24	esv3419951	chr15:31157739-31165597	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2177669	RP11-540B6.2	cis	Whole Blood	GTEx
rs2177669	RP11-540B6.2	cis	lung	GTEx
rs2177669	RP11-540B6.3	cis	lung	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31127200-31170000	Weak transcription	Pancreas	Pancrea
2	chr15:31132800-31195600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:31152600-31163600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:31157200-31163400	Weak transcription	Dnd41	blood
5	chr15:31157400-31177600	Weak transcription	Spleen	Spleen
6	chr15:31158200-31161600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:31159000-31173800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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