Variant report

Variant	rs6115094
Chromosome Location	chr20:25210827-25210828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25209701-25211277	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr20:25210654-25211117	H1-neurons	neurons:	n/a	n/a
3	TCF7L2	chr20:25210553-25211035	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr20:25210685-25211182	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:25210677-25211104	H1-neurons	neurons:	n/a	n/a
6	GATA3	chr20:25210634-25210980	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:25210678..25212616-chr20:25212688..25215321,2	MCF-7	breast:
2	chr20:25209487..25211779-chr20:25212504..25214793,2	MCF-7	breast:
3	chr20:25209268..25211969-chr20:25218955..25220793,2	MCF-7	breast:
4	chr20:25209269..25211589-chr20:25226481..25229322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268302	TF binding region
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1007708	0.80[ASN][1000 genomes]
rs1044573	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077889	0.80[ASN][1000 genomes]
rs11087505	0.80[ASN][1000 genomes]
rs11100	0.85[CHB][hapmap]
rs1118963	1.00[ASN][1000 genomes]
rs1130694	0.82[CHB][hapmap]
rs11699953	0.89[EUR][1000 genomes]
rs1473695	0.85[CHB][hapmap]
rs1555330	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888997	0.82[CHB][hapmap]
rs1888999	0.82[CHB][hapmap]
rs2145126	0.80[ASN][1000 genomes]
rs2227890	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2227892	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2257233	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2257432	0.80[ASN][1000 genomes]
rs2257461	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2257464	0.80[ASN][1000 genomes]
rs2257705	0.80[ASN][1000 genomes]
rs2257712	0.80[ASN][1000 genomes]
rs2257808	0.80[ASN][1000 genomes]
rs2257809	0.80[ASN][1000 genomes]
rs2257982	0.80[ASN][1000 genomes]
rs2257985	0.80[ASN][1000 genomes]
rs2257991	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2258066	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2258135	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2258201	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2258617	0.82[CHB][hapmap]
rs2258719	0.82[CHB][hapmap]
rs2258728	0.82[CHB][hapmap]
rs2258769	1.00[CHB][hapmap]
rs2259837	0.82[CHB][hapmap]
rs2260997	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs2261109	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2261115	0.80[ASN][1000 genomes]
rs2261698	0.80[ASN][1000 genomes]
rs2261720	0.80[ASN][1000 genomes]
rs2261747	0.82[CHB][hapmap]
rs2261753	0.80[ASN][1000 genomes]
rs2261784	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2261785	0.80[ASN][1000 genomes]
rs2261790	0.80[ASN][1000 genomes]
rs2261794	0.80[ASN][1000 genomes]
rs2273473	0.84[EUR][1000 genomes]
rs2297496	0.82[CHB][hapmap]
rs2297497	0.82[CHB][hapmap]
rs2387881	0.82[CHB][hapmap]
rs2424698	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs2424699	0.85[CHB][hapmap]
rs2424700	0.80[ASN][1000 genomes]
rs2424704	0.82[CHB][hapmap]
rs2474766	1.00[ASN][1000 genomes]
rs2474769	1.00[ASN][1000 genomes]
rs2474777	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2482911	0.82[CHB][hapmap]
rs2482923	0.82[CHB][hapmap]
rs2482927	0.85[CHB][hapmap]
rs2482931	0.82[CHB][hapmap]
rs2482943	0.85[CHB][hapmap]
rs2500399	0.85[CHB][hapmap]
rs2500405	0.82[CHB][hapmap]
rs2500406	0.82[CHB][hapmap]
rs2500424	1.00[CHB][hapmap]
rs2500432	0.82[CHB][hapmap]
rs2500433	0.82[CHB][hapmap]
rs2500436	1.00[CHB][hapmap]
rs2500446	0.82[CHB][hapmap]
rs3002702	0.80[ASN][1000 genomes]
rs33999482	0.80[ASN][1000 genomes]
rs3746337	0.88[CEU][hapmap];0.82[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761117	0.82[CHB][hapmap]
rs4619688	1.00[ASN][1000 genomes]
rs4813562	0.82[CHB][hapmap]
rs4815411	0.82[CHB][hapmap]
rs4815412	0.82[CHB][hapmap]
rs4815417	0.82[CHB][hapmap]
rs6037062	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6037069	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6037095	0.82[CHB][hapmap]
rs6037097	0.82[CHB][hapmap]
rs6037103	0.82[CHB][hapmap]
rs6037105	0.82[CHB][hapmap]
rs6050439	0.80[ASN][1000 genomes]
rs6050442	0.80[ASN][1000 genomes]
rs6050445	0.80[ASN][1000 genomes]
rs6050463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050464	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050472	0.84[ASN][1000 genomes]
rs6050477	0.84[ASN][1000 genomes]
rs6050481	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs6050482	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050532	1.00[CHB][hapmap]
rs6050544	1.00[CHB][hapmap]
rs6050559	0.82[CHB][hapmap]
rs6050561	0.82[CHB][hapmap]
rs6050565	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6050567	0.82[CHB][hapmap]
rs6050573	0.82[CHB][hapmap]
rs6050590	0.85[CHB][hapmap]
rs6050598	0.82[CHB][hapmap]
rs6050599	0.85[CHB][hapmap]
rs6076336	0.82[CHB][hapmap]
rs6083804	1.00[CHB][hapmap]
rs6083805	0.82[CHB][hapmap]
rs6083809	1.00[CHB][hapmap]
rs6083818	0.82[CHB][hapmap]
rs6083828	0.82[CHB][hapmap]
rs6083853	0.82[CHB][hapmap]
rs6107015	0.80[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6107017	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107019	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107031	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6115093	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115100	1.00[ASN][1000 genomes]
rs6115101	0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs6115109	1.00[ASN][1000 genomes]
rs6115140	0.82[CHB][hapmap]
rs6115159	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs6132819	0.82[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132820	1.00[ASN][1000 genomes]
rs6132821	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132822	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6132824	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138537	0.82[CHB][hapmap]
rs6138545	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6138546	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138550	1.00[ASN][1000 genomes]
rs6138553	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs6138555	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138556	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs7020	0.82[CHB][hapmap]
rs7267979	0.82[CHB][hapmap]
rs7453	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115257	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8184820	0.80[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910996	0.80[ASN][1000 genomes]
rs910997	0.80[ASN][1000 genomes]
rs9927	0.82[CHB][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	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6115094	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6115094	ABHD12	cis	Artery Tibial	GTEx
rs6115094	PYGB	cis	Whole Blood	GTEx
rs6115094	PYGB	cis	multi-tissue	Pritchard
rs6115094	ABHD12	cis	Cerebellum	GTEx
rs6115094	ABHD12	cis	multi-tissue	Pritchard
rs6115094	ABHD12	cis	Temporal Cortex	GTEx
rs6115094	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6115094	ABHD12	cis	Brain Pons	GTEx
rs6115094	ABHD12	cis	Frontal Cortex	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr20:25198000-25214000	Weak transcription	Fetal Lung	lung
3	chr20:25198400-25212200	Enhancers	Fetal Heart	heart
4	chr20:25199000-25212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr20:25199200-25212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr20:25204200-25213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr20:25204400-25218200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr20:25204800-25213600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr20:25206200-25211400	Enhancers	Right Atrium	heart
11	chr20:25206600-25214000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr20:25206800-25212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr20:25206800-25218200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr20:25207200-25212600	Weak transcription	Brain Germinal Matrix	brain
15	chr20:25207200-25213800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr20:25207200-25213800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr20:25207400-25211000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr20:25207400-25213200	Weak transcription	Fetal Thymus	thymus
19	chr20:25207800-25218200	Weak transcription	Spleen	Spleen
20	chr20:25207800-25218200	Weak transcription	Dnd41	blood
21	chr20:25208000-25212200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr20:25208000-25212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr20:25208400-25212200	Weak transcription	Primary T cells from cord blood	blood
24	chr20:25208400-25213400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:25208400-25213600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr20:25208400-25214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:25208400-25214000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr20:25208400-25214000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr20:25208400-25214000	Weak transcription	Placenta	Placenta
30	chr20:25208400-25214200	Weak transcription	Brain Substantia Nigra	brain
31	chr20:25208600-25211800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:25208600-25211800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr20:25208600-25213200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr20:25208600-25213200	Weak transcription	Hela-S3	cervix
35	chr20:25208600-25213400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr20:25208600-25213400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr20:25208600-25213400	Weak transcription	Ovary	ovary
38	chr20:25208600-25213400	Weak transcription	HMEC	breast
39	chr20:25208600-25213400	Weak transcription	Osteobl	bone
40	chr20:25208600-25213600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr20:25208600-25213600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr20:25208600-25213600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:25208600-25213600	Weak transcription	Liver	Liver
44	chr20:25208600-25213800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr20:25208600-25213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr20:25208600-25213800	Weak transcription	Esophagus	oesophagus
47	chr20:25208600-25213800	Weak transcription	Fetal Intestine Large	intestine
48	chr20:25208600-25213800	Weak transcription	HSMM	muscle
49	chr20:25208600-25213800	Weak transcription	HSMMtube	muscle
50	chr20:25208600-25213800	Weak transcription	NHLF	lung

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