Variant report

Variant	rs6050427
Chromosome Location	chr20:25181074-25181075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25175993..25177808-chr20:25179457..25181859,3	K562	blood:
2	chr20:25180384..25184358-chr20:25185233..25189796,6	K562	blood:
3	chr20:25176534..25179250-chr20:25179296..25181376,2	MCF-7	breast:
4	chr20:25180225..25182029-chr20:25219353..25221557,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1007707	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1007708	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1044573	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11087505	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11100	1.00[JPT][hapmap]
rs1130694	1.00[JPT][hapmap]
rs11698185	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs13038092	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs1473695	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1888997	1.00[JPT][hapmap]
rs1888999	1.00[JPT][hapmap]
rs2227890	1.00[JPT][hapmap]
rs2227892	1.00[JPT][hapmap]
rs2257233	1.00[JPT][hapmap]
rs2257461	1.00[JPT][hapmap]
rs2257705	1.00[JPT][hapmap]
rs2257712	1.00[JPT][hapmap]
rs2257991	1.00[JPT][hapmap]
rs2258066	1.00[JPT][hapmap]
rs2258135	1.00[JPT][hapmap]
rs2258201	1.00[JPT][hapmap]
rs2258617	1.00[JPT][hapmap]
rs2258719	1.00[JPT][hapmap]
rs2258728	1.00[JPT][hapmap]
rs2258769	1.00[JPT][hapmap]
rs2259837	1.00[JPT][hapmap]
rs2260997	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2261109	1.00[JPT][hapmap]
rs2261747	1.00[JPT][hapmap]
rs2261784	1.00[JPT][hapmap]
rs2268879	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2297496	1.00[JPT][hapmap]
rs2297497	1.00[JPT][hapmap]
rs2387881	1.00[JPT][hapmap]
rs2424698	1.00[JPT][hapmap]
rs2424699	1.00[JPT][hapmap]
rs2424704	1.00[JPT][hapmap]
rs2474777	1.00[JPT][hapmap]
rs2482923	1.00[JPT][hapmap]
rs2482927	1.00[JPT][hapmap]
rs2482931	1.00[JPT][hapmap]
rs2482943	1.00[JPT][hapmap]
rs2500399	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2500405	1.00[JPT][hapmap]
rs2500432	1.00[JPT][hapmap]
rs2500433	1.00[JPT][hapmap]
rs2500446	1.00[JPT][hapmap]
rs3746337	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4813562	1.00[JPT][hapmap]
rs4815411	1.00[JPT][hapmap]
rs4815412	1.00[JPT][hapmap]
rs4815417	1.00[JPT][hapmap]
rs6037057	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6037059	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6037095	1.00[JPT][hapmap]
rs6037097	1.00[JPT][hapmap]
rs6037103	1.00[JPT][hapmap]
rs6037105	1.00[JPT][hapmap]
rs6050422	0.85[CHB][hapmap];0.80[YRI][hapmap]
rs6050425	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6050426	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6050429	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6050431	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6050432	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6050439	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6050442	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6050445	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6050477	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6050513	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6050515	0.85[JPT][hapmap]
rs6050532	1.00[JPT][hapmap]
rs6050544	0.86[JPT][hapmap]
rs6050559	1.00[JPT][hapmap]
rs6050561	1.00[JPT][hapmap]
rs6050565	1.00[JPT][hapmap]
rs6050567	1.00[JPT][hapmap]
rs6050573	1.00[JPT][hapmap]
rs6076336	1.00[JPT][hapmap]
rs6083776	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]
rs6083779	0.81[AFR][1000 genomes]
rs6083804	1.00[JPT][hapmap]
rs6083805	1.00[JPT][hapmap]
rs6083809	1.00[JPT][hapmap]
rs6083818	1.00[JPT][hapmap]
rs6083828	1.00[JPT][hapmap]
rs6107015	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6107031	1.00[JPT][hapmap]
rs6115093	1.00[JPT][hapmap]
rs6115101	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6115140	1.00[JPT][hapmap]
rs6115159	1.00[JPT][hapmap]
rs6132819	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6138536	0.90[ASN][1000 genomes]
rs6138537	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6138553	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6138556	1.00[JPT][hapmap]
rs7020	1.00[JPT][hapmap]
rs7267979	1.00[JPT][hapmap]
rs7453	0.82[ASW][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs8115257	0.82[ASW][hapmap];1.00[JPT][hapmap]
rs8124539	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs8184820	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs9927	1.00[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6050427	ENTPD6	cis	parietal	SCAN
rs6050427	NANP	cis	cerebellum	SCAN
rs6050427	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6050427	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6050427	NINL	cis	Artery Aorta	GTEx
rs6050427	NINL	cis	cerebellum	SCAN
rs6050427	ABHD12	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 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	chr20:25177800-25184400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr20:25177800-25185200	Weak transcription	Placenta	Placenta
4	chr20:25177800-25191600	Weak transcription	NH-A	brain
5	chr20:25178000-25184000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr20:25178000-25192600	Weak transcription	Fetal Lung	lung
7	chr20:25178200-25184200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr20:25178200-25185400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr20:25178200-25185800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr20:25178200-25187800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr20:25178200-25192000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr20:25178200-25192000	Weak transcription	Aorta	Aorta
13	chr20:25178400-25181200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr20:25178400-25183400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr20:25178400-25183400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr20:25178400-25184000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr20:25178400-25184000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr20:25178400-25184400	Weak transcription	Osteobl	bone
19	chr20:25178400-25184800	Weak transcription	Stomach Mucosa	stomach
20	chr20:25178400-25190400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr20:25178400-25203800	Weak transcription	Small Intestine	intestine
22	chr20:25178400-25203800	Weak transcription	Hela-S3	cervix
23	chr20:25178600-25181400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr20:25178600-25181600	Enhancers	Fetal Heart	heart
25	chr20:25178600-25183400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr20:25178600-25183600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr20:25178600-25184000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:25178600-25185200	Weak transcription	Fetal Intestine Large	intestine
29	chr20:25178600-25185800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr20:25178600-25185800	Weak transcription	Spleen	Spleen
31	chr20:25178600-25186400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr20:25178600-25187400	Weak transcription	Liver	Liver
33	chr20:25178600-25190400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr20:25178600-25190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr20:25178600-25195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr20:25178600-25200400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr20:25178600-25212200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr20:25178800-25181600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr20:25178800-25184200	Weak transcription	Brain Substantia Nigra	brain
40	chr20:25178800-25187600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr20:25179600-25181400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr20:25179800-25182600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr20:25179800-25185200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:25179800-25185600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr20:25179800-25185600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr20:25179800-25190600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr20:25180000-25181800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr20:25180000-25184400	Weak transcription	Pancreas	Pancrea
49	chr20:25180000-25184600	Weak transcription	Brain Hippocampus Middle	brain
50	chr20:25180000-25185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links