Variant report

Variant	rs13038092
Chromosome Location	chr20:25249734-25249735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25248981..25251939-chr20:25255782..25258389,2	MCF-7	breast:
2	chr20:25237526..25240142-chr20:25247989..25249808,2	K562	blood:
3	chr20:25248500..25251433-chr20:25251718..25254051,3	MCF-7	breast:

Extended variants
information (count: 156 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:140)

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]
rs1473695	0.86[JPT][hapmap]
rs16987767	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];0.88[YRI][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	0.87[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	1.00[ASN][1000 genomes]
rs397119	1.00[JPT][hapmap]
rs398036	1.00[JPT][hapmap]
rs401166	1.00[JPT][hapmap]
rs422844	1.00[JPT][hapmap]
rs454723	1.00[JPT][hapmap]
rs45587239	0.87[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]
rs59242979	0.97[AFR][1000 genomes]
rs60043588	0.97[AFR][1000 genomes];1.00[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]
rs6050472	0.91[ASN][1000 genomes]
rs6050477	1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs6050513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs6050515	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[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	0.97[AFR][1000 genomes];1.00[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[CHB][hapmap]
rs66650433	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67049380	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67352161	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67864609	1.00[ASN][1000 genomes]
rs67867367	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs67920646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7020	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7267979	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7269584	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7270835	1.00[JPT][hapmap]
rs7274130	0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73612661	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73612664	0.80[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[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.87[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:16 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13038092	ZNF337	cis	cerebellum	SCAN
rs13038092	ZNF337	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25229800-25250000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:25231200-25251800	Weak transcription	Hela-S3	cervix
4	chr20:25231200-25252200	Weak transcription	HUVEC	blood vessel
5	chr20:25231400-25249800	Weak transcription	Small Intestine	intestine
6	chr20:25233200-25252200	Weak transcription	Fetal Brain Male	brain
7	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
8	chr20:25236200-25251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr20:25236600-25253800	Weak transcription	Psoas Muscle	Psoas
10	chr20:25237600-25249800	Weak transcription	NHDF-Ad	bronchial
11	chr20:25237600-25262800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr20:25238000-25249800	Weak transcription	Liver	Liver
13	chr20:25238000-25250000	Weak transcription	Placenta	Placenta
14	chr20:25239600-25249800	Weak transcription	Pancreas	Pancrea
15	chr20:25239800-25249800	Weak transcription	Gastric	stomach
16	chr20:25240800-25249800	Weak transcription	Brain Anterior Caudate	brain
17	chr20:25240800-25249800	Weak transcription	Colon Smooth Muscle	Colon
18	chr20:25240800-25249800	Weak transcription	Ovary	ovary
19	chr20:25240800-25249800	Weak transcription	GM12878-XiMat	blood
20	chr20:25240800-25251400	Weak transcription	Thymus	Thymus
21	chr20:25241000-25249800	Weak transcription	Fetal Heart	heart
22	chr20:25241000-25258200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr20:25241400-25249800	Weak transcription	Fetal Lung	lung
24	chr20:25241400-25249800	Weak transcription	HSMMtube	muscle
25	chr20:25241400-25251600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr20:25241400-25252600	Weak transcription	Primary B cells from cord blood	blood
27	chr20:25241600-25249800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr20:25241600-25249800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr20:25241600-25250000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr20:25241600-25250000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:25241600-25250200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr20:25241600-25251800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr20:25241800-25249800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr20:25241800-25249800	Weak transcription	Brain Angular Gyrus	brain
35	chr20:25241800-25249800	Weak transcription	Brain Hippocampus Middle	brain
36	chr20:25241800-25249800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr20:25241800-25273200	Weak transcription	Stomach Mucosa	stomach
38	chr20:25242000-25249800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr20:25242000-25249800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:25242000-25249800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr20:25242000-25249800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr20:25242000-25249800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr20:25242000-25249800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr20:25242000-25249800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr20:25242000-25249800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr20:25242000-25249800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr20:25242000-25249800	Weak transcription	Aorta	Aorta
48	chr20:25242000-25249800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr20:25242000-25249800	Weak transcription	Brain Germinal Matrix	brain
50	chr20:25242000-25249800	Weak transcription	Esophagus	oesophagus

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