Variant report

Variant	rs6050513
Chromosome Location	chr20:25254688-25254689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25252960..25255983-chr20:25260897..25264213,3	MCF-7	breast:
2	chr20:24973494..24975181-chr20:25253726..25255240,2	MCF-7	breast:
3	chr20:25253122..25255377-chr20:25264937..25266840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1007707	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1044573	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1047171	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11087521	1.00[JPT][hapmap]
rs11100	1.00[JPT][hapmap]
rs1130694	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11698185	0.86[JPT][hapmap]
rs11699203	1.00[JPT][hapmap]
rs12428	1.00[JPT][hapmap]
rs13038092	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs1473695	0.86[JPT][hapmap]
rs16987767	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs1888997	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs1888999	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2151144	1.00[JPT][hapmap]
rs2227890	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2227892	1.00[JPT][hapmap]
rs2227894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2257233	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2257461	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2257705	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2257712	1.00[JPT][hapmap]
rs2257991	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258066	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258135	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258201	1.00[JPT][hapmap]
rs2258617	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258719	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258728	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2258769	1.00[JPT][hapmap]
rs2259837	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2260997	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2261109	1.00[JPT][hapmap]
rs2261747	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2261784	1.00[JPT][hapmap]
rs2268879	1.00[JPT][hapmap]
rs2297496	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2297497	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2387881	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2424698	1.00[JPT][hapmap]
rs2424699	1.00[JPT][hapmap]
rs2424704	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2474777	1.00[JPT][hapmap]
rs2482911	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2482918	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2482923	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2482927	1.00[JPT][hapmap]
rs2482931	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2482943	1.00[JPT][hapmap]
rs2500399	1.00[JPT][hapmap]
rs2500405	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2500406	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2500424	1.00[JPT][hapmap]
rs2500432	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2500433	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2500436	1.00[JPT][hapmap]
rs2500446	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs2856	1.00[JPT][hapmap]
rs3746337	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3761117	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs3787079	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs397119	1.00[JPT][hapmap]
rs398036	1.00[JPT][hapmap]
rs401166	1.00[JPT][hapmap]
rs422844	1.00[JPT][hapmap]
rs449370	1.00[JPT][hapmap]
rs454723	1.00[JPT][hapmap]
rs45587239	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813562	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4815411	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4815412	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4815417	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs58351126	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59242979	0.88[EUR][1000 genomes]
rs60043588	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6037095	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6037097	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6037103	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6037105	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050425	1.00[JPT][hapmap]
rs6050427	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6050431	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6050477	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs6050515	1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050532	1.00[JPT][hapmap]
rs6050544	0.86[JPT][hapmap]
rs6050559	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050561	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050565	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050567	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050573	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050590	1.00[JPT][hapmap]
rs6050598	1.00[JPT][hapmap]
rs6050599	1.00[JPT][hapmap]
rs6050611	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6050626	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6076336	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6083776	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6083804	1.00[JPT][hapmap]
rs6083805	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6083809	1.00[JPT][hapmap]
rs6083818	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6083828	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6083853	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6083862	0.86[JPT][hapmap]
rs6107015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6107031	1.00[JPT][hapmap]
rs6107045	1.00[JPT][hapmap]
rs6107047	1.00[JPT][hapmap]
rs6115093	1.00[JPT][hapmap]
rs6115101	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6115140	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6115159	1.00[JPT][hapmap]
rs6115191	1.00[JPT][hapmap]
rs61272267	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6132819	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138537	0.86[JPT][hapmap]
rs6138553	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138556	1.00[JPT][hapmap]
rs6138572	1.00[JPT][hapmap]
rs6138575	1.00[JPT][hapmap]
rs6515626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66650433	0.87[ASN][1000 genomes]
rs67049380	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67184896	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67352161	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67864609	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67867367	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7267979	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7269584	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7270835	1.00[JPT][hapmap]
rs7272959	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7274130	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73598373	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73612661	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73612664	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73612665	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73614590	0.81[ASN][1000 genomes]
rs7453	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs761025	1.00[JPT][hapmap]
rs8115257	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs8124539	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8184820	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9927	0.89[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6050513	RP4-694B14.5	cis	Adipose Subcutaneous	GTEx
rs6050513	ZNF337	cis	lung	GTEx
rs6050513	ZNF337	cis	Adipose Subcutaneous	GTEx
rs6050513	ZNF337	Cis_1M	lymphoblastoid	RTeQTL
rs6050513	ZNF337	cis	lymphoblastoid	seeQTL
rs6050513	RP4-694B14.5	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25237600-25262800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:25241000-25258200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr20:25241800-25273200	Weak transcription	Stomach Mucosa	stomach
6	chr20:25242800-25258000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:25243000-25269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr20:25246800-25259400	Strong transcription	HMEC	breast
9	chr20:25247400-25258000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:25249000-25255400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:25249200-25256400	Strong transcription	HSMM	muscle
14	chr20:25249200-25274800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:25249200-25275000	Strong transcription	A549	lung
16	chr20:25249200-25285800	Strong transcription	Dnd41	blood
17	chr20:25249400-25256000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr20:25249400-25262000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr20:25249400-25274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr20:25249400-25274800	Strong transcription	Osteobl	bone
21	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
22	chr20:25249600-25255400	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr20:25249600-25255800	Genic enhancers	Left Ventricle	heart
24	chr20:25249600-25258400	Strong transcription	HepG2	liver
25	chr20:25249600-25261400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr20:25249600-25261800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr20:25249600-25267000	Strong transcription	NH-A	brain
28	chr20:25249600-25273400	Strong transcription	NHEK	skin
29	chr20:25249600-25274400	Strong transcription	Lung	lung
30	chr20:25249600-25274600	Strong transcription	Primary T cells from cord blood	blood
31	chr20:25249600-25274600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr20:25249600-25274800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr20:25249600-25275000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr20:25249600-25275000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr20:25249600-25275000	Strong transcription	NHLF	lung
36	chr20:25249600-25275200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr20:25249800-25254800	Enhancers	Fetal Heart	heart
42	chr20:25249800-25255000	Strong transcription	Fetal Lung	lung
43	chr20:25249800-25255200	Strong transcription	NHDF-Ad	bronchial
44	chr20:25249800-25256400	Strong transcription	Ovary	ovary
45	chr20:25249800-25256800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr20:25249800-25258800	Strong transcription	Colonic Mucosa	Colon
47	chr20:25249800-25260600	Strong transcription	Spleen	Spleen
48	chr20:25249800-25261000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr20:25249800-25261800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr20:25249800-25262000	Strong transcription	Fetal Muscle Leg	muscle

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