Variant report

Variant	rs6138537
Chromosome Location	chr20:25184466-25184467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr20:25184448-25184812	GM12878	blood:	n/a	n/a
2	IKZF1	chr20:25184465-25185005	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25183731..25186136-chr20:25238166..25239977,2	MCF-7	breast:
2	chr20:25182714..25185445-chr20:25216908..25218844,2	MCF-7	breast:
3	chr20:25176013..25179017-chr20:25181894..25184717,4	K562	blood:
4	chr20:25184070..25187780-chr20:25226267..25231211,5	MCF-7	breast:
5	chr20:25183254..25185690-chr20:25227240..25230153,3	MCF-7	breast:
6	chr20:25183250..25185573-chr20:25216058..25218999,2	K562	blood:

No data

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

Extended variants
information (count: 119 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1007707	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1007708	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1044573	0.86[JPT][hapmap]
rs11087505	0.90[ASN][1000 genomes]
rs11100	0.86[JPT][hapmap]
rs1130694	0.86[JPT][hapmap]
rs11698185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11699392	0.90[LWK][hapmap]
rs13038092	0.86[JPT][hapmap]
rs1473695	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[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	0.86[JPT][hapmap]
rs2261109	0.86[JPT][hapmap]
rs2261747	0.86[JPT][hapmap]
rs2261784	0.86[JPT][hapmap]
rs2268879	0.85[CEU][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];0.84[JPT][hapmap]
rs2500405	0.86[JPT][hapmap]
rs2500432	0.86[JPT][hapmap]
rs2500433	0.86[JPT][hapmap]
rs2500446	0.86[JPT][hapmap]
rs3746337	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	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037059	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	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[MEX][hapmap]
rs6050425	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6050426	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050427	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6050429	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050431	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];0.95[ASN][1000 genomes]
rs6050432	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050439	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050442	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6050445	0.90[ASN][1000 genomes]
rs6050513	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]
rs6076336	0.86[JPT][hapmap]
rs6083776	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]
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	0.86[JPT][hapmap]
rs6107031	0.86[JPT][hapmap]
rs6115093	0.86[JPT][hapmap]
rs6115094	0.82[CHB][hapmap]
rs6115101	0.86[JPT][hapmap]
rs6115140	0.86[JPT][hapmap]
rs6115159	0.86[JPT][hapmap]
rs6132819	0.86[JPT][hapmap]
rs6138536	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138553	0.86[JPT][hapmap]
rs6138556	0.86[JPT][hapmap]
rs7020	0.86[JPT][hapmap]
rs7267979	0.86[JPT][hapmap]
rs7453	0.86[JPT][hapmap]
rs8115257	0.86[JPT][hapmap]
rs8124539	0.86[JPT][hapmap]
rs8184820	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6138537	NINL	cis	cerebellum	SCAN
rs6138537	PYGB	cis	Whole Blood	GTEx
rs6138537	ABHD12	cis	Cerebellum	GTEx
rs6138537	CSTL1	cis	cerebellum	SCAN
rs6138537	ABHD12	cis	cerebellum	SCAN
rs6138537	ABHD12	cis	Brain Pons	GTEx
rs6138537	ABHD12	cis	Nerve Tibial	GTEx
rs6138537	PYGB	cis	cerebellum	SCAN
rs6138537	ABHD12	cis	Artery Tibial	GTEx
rs6138537	ENTPD6	cis	parietal	SCAN
rs6138537	ABHD12	cis	Temporal Cortex	GTEx
rs6138537	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6138537	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6138537	NINL	cis	parietal	SCAN
rs6138537	ABHD12	cis	Frontal Cortex	GTEx
rs6138537	PYGB	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 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	chr20:25177800-25185200	Weak transcription	Placenta	Placenta
3	chr20:25177800-25191600	Weak transcription	NH-A	brain
4	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
5	chr20:25178200-25185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:25178200-25185800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr20:25178200-25187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
10	chr20:25178400-25184800	Weak transcription	Stomach Mucosa	stomach
11	chr20:25178400-25190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
13	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
14	chr20:25178600-25185200	Weak transcription	Fetal Intestine Large	intestine
15	chr20:25178600-25185800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr20:25178600-25185800	Weak transcription	Spleen	Spleen
17	chr20:25178600-25186400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr20:25178600-25187400	Weak transcription	Liver	Liver
19	chr20:25178600-25190400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr20:25178600-25190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr20:25178600-25195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr20:25178800-25187600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:25179800-25185200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:25179800-25185600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr20:25179800-25185600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr20:25179800-25190600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr20:25180000-25184600	Weak transcription	Brain Hippocampus Middle	brain
30	chr20:25180000-25185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:25180000-25185200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr20:25180000-25185200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr20:25180000-25185200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr20:25180000-25185200	Weak transcription	Fetal Muscle Leg	muscle
35	chr20:25180000-25185200	Weak transcription	Fetal Stomach	stomach
36	chr20:25180000-25185200	Weak transcription	Right Atrium	heart
37	chr20:25180000-25185600	Weak transcription	Fetal Intestine Small	intestine
38	chr20:25180000-25187400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr20:25180000-25191800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:25180000-25192200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr20:25180000-25207600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr20:25180200-25184600	Weak transcription	Dnd41	blood
43	chr20:25180200-25185200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr20:25180200-25185200	Weak transcription	Fetal Thymus	thymus
45	chr20:25180200-25185200	Weak transcription	Right Ventricle	heart
46	chr20:25180200-25185400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr20:25180200-25185400	Weak transcription	Adipose Nuclei	Adipose
48	chr20:25180200-25185600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr20:25180200-25185800	Weak transcription	Primary T cells from cord blood	blood
50	chr20:25180200-25185800	Weak transcription	Gastric	stomach

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