Variant report

Variant	rs6083776
Chromosome Location	chr20:25186116-25186117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25185984-25186994	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25183731..25186136-chr20:25238166..25239977,2	MCF-7	breast:
2	chr20:25175543..25177145-chr20:25184503..25186642,2	MCF-7	breast:
3	chr20:25185473..25187365-chr20:25194994..25197584,2	K562	blood:
4	chr20:25184070..25187780-chr20:25226267..25231211,5	MCF-7	breast:
5	chr20:25185632..25187734-chr20:25204064..25206266,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENTPD6	TF binding region
ENSG00000100994	Chromatin interaction
ENSG00000202414	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1007707	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1007708	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1044573	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs11087505	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11100	0.86[JPT][hapmap]
rs1130694	0.86[JPT][hapmap]
rs11698185	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13038092	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1473695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888997	0.86[JPT][hapmap]
rs1888999	0.86[JPT][hapmap]
rs2227890	0.86[JPT][hapmap]
rs2227892	0.86[JPT][hapmap]
rs2257233	0.86[JPT][hapmap]
rs2257461	0.86[JPT][hapmap]
rs2257705	0.86[JPT][hapmap]
rs2257712	0.86[JPT][hapmap]
rs2257991	0.86[JPT][hapmap]
rs2258066	0.86[JPT][hapmap]
rs2258135	0.86[JPT][hapmap]
rs2258201	0.86[JPT][hapmap]
rs2258617	0.86[JPT][hapmap]
rs2258719	0.86[JPT][hapmap]
rs2258728	0.86[JPT][hapmap]
rs2258769	0.86[JPT][hapmap]
rs2259837	0.86[JPT][hapmap]
rs2260997	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2261109	0.86[JPT][hapmap]
rs2261747	0.86[JPT][hapmap]
rs2261784	0.86[JPT][hapmap]
rs2268879	0.81[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2297496	0.86[JPT][hapmap]
rs2297497	0.86[JPT][hapmap]
rs2387881	0.86[JPT][hapmap]
rs2424698	0.86[JPT][hapmap]
rs2424699	0.86[JPT][hapmap]
rs2424704	0.86[JPT][hapmap]
rs2474777	0.86[JPT][hapmap]
rs2482923	0.86[JPT][hapmap]
rs2482927	0.86[JPT][hapmap]
rs2482931	0.86[JPT][hapmap]
rs2482943	0.86[JPT][hapmap]
rs2500399	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2500405	0.86[JPT][hapmap]
rs2500432	0.86[JPT][hapmap]
rs2500433	0.86[JPT][hapmap]
rs2500446	0.86[JPT][hapmap]
rs3746337	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4813562	0.86[JPT][hapmap]
rs4815411	0.86[JPT][hapmap]
rs4815412	0.86[JPT][hapmap]
rs4815417	0.86[JPT][hapmap]
rs6037057	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037059	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6037095	0.86[JPT][hapmap]
rs6037097	0.86[JPT][hapmap]
rs6037103	0.86[JPT][hapmap]
rs6037105	0.86[JPT][hapmap]
rs6050422	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs6050425	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs6050426	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050427	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6050429	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050431	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050432	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050439	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050442	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050445	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050477	0.81[CHD][hapmap]
rs6050513	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6050532	0.86[JPT][hapmap]
rs6050559	0.86[JPT][hapmap]
rs6050561	0.86[JPT][hapmap]
rs6050565	0.86[JPT][hapmap]
rs6050567	0.86[JPT][hapmap]
rs6050573	0.86[JPT][hapmap]
rs6050590	0.86[JPT][hapmap]
rs6076336	0.86[JPT][hapmap]
rs6083779	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6083804	0.86[JPT][hapmap]
rs6083805	0.86[JPT][hapmap]
rs6083809	0.86[JPT][hapmap]
rs6083818	0.86[JPT][hapmap]
rs6083828	0.86[JPT][hapmap]
rs6107015	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6107031	0.86[JPT][hapmap]
rs6115093	0.86[JPT][hapmap]
rs6115101	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6115140	0.86[JPT][hapmap]
rs6115159	0.86[JPT][hapmap]
rs6132819	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6138536	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138537	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138553	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6138556	0.86[JPT][hapmap]
rs7020	0.86[JPT][hapmap]
rs7267979	0.86[JPT][hapmap]
rs7453	0.82[ASW][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs8115257	0.82[ASW][hapmap];0.86[JPT][hapmap]
rs8124539	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs8184820	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs9927	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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
18	nsv3340	chr20:25160137-25190540	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6083776	ABHD12	trans	brain	seeQTL
rs6083776	ABHD12	cis	Brain Pons	GTEx
rs6083776	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6083776	ABHD12	cis	multi-tissue	Pritchard
rs6083776	ABHD12	cis	lymphoblastoid	seeQTL
rs6083776	ABHD12	cis	Nerve Tibial	GTEx
rs6083776	CSTL1	cis	cerebellum	SCAN
rs6083776	NINL	cis	parietal	SCAN
rs6083776	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6083776	ENTPD6	cis	parietal	SCAN
rs6083776	ENTPD6	cis	multi-tissue	Pritchard
rs6083776	ABHD12	cis	Temporal Cortex	GTEx
rs6083776	ABHD12	cis	Cerebellum	GTEx
rs6083776	ABHD12	cis	brain	seeQTL
rs6083776	ABHD12	cis	Frontal Cortex	GTEx
rs6083776	ABHD12	cis	cerebellum	SCAN
rs6083776	NINL	cis	cerebellum	SCAN
rs6083776	PYGB	cis	multi-tissue	Pritchard
rs6083776	PYGB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25177600-25190400	Weak transcription	HUVEC	blood vessel
2	chr20:25177800-25191600	Weak transcription	NH-A	brain
3	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
4	chr20:25178200-25187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
7	chr20:25178400-25190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
9	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
10	chr20:25178600-25186400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr20:25178600-25187400	Weak transcription	Liver	Liver
12	chr20:25178600-25190400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:25178600-25190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:25178600-25195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr20:25178800-25187600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr20:25179800-25190600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr20:25180000-25187400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr20:25180000-25191800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr20:25180000-25192200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:25180200-25187800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:25180400-25186600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr20:25180400-25192000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr20:25180600-25191600	Weak transcription	HSMMtube	muscle
27	chr20:25180800-25186200	Weak transcription	NHLF	lung
28	chr20:25180800-25190600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:25180800-25190600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr20:25180800-25191000	Weak transcription	HSMM	muscle
31	chr20:25180800-25191600	Weak transcription	NHDF-Ad	bronchial
32	chr20:25180800-25196000	Weak transcription	Psoas Muscle	Psoas
33	chr20:25180800-25196200	Weak transcription	Fetal Brain Male	brain
34	chr20:25181000-25187000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr20:25181000-25190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr20:25181200-25190400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr20:25181400-25190400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr20:25181800-25190600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr20:25181800-25202000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr20:25182000-25190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr20:25182600-25190400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr20:25183200-25186800	Enhancers	Fetal Heart	heart
43	chr20:25183400-25186600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr20:25183400-25187000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr20:25184000-25186200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr20:25184000-25190600	Weak transcription	Colon Smooth Muscle	Colon
47	chr20:25184000-25190600	Weak transcription	Fetal Brain Female	brain
48	chr20:25184200-25186200	Enhancers	Brain Substantia Nigra	brain
49	chr20:25184200-25187000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr20:25184200-25188000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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