Variant report

Variant	rs6050425
Chromosome Location	chr20:25178119-25178120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25174010..25179528-chr20:25225802..25231331,13	MCF-7	breast:
2	chr20:25174902..25179249-chr20:25225017..25231959,9	MCF-7	breast:
3	chr20:25176590..25179411-chr20:25196913..25199010,2	MCF-7	breast:
4	chr20:25173813..25179807-chr20:25203379..25207002,9	MCF-7	breast:
5	chr20:25177563..25180784-chr20:25185797..25188604,4	MCF-7	breast:
6	chr20:24971936..24974944-chr20:25175039..25178381,3	MCF-7	breast:
7	chr20:25176534..25179250-chr20:25179296..25181376,2	MCF-7	breast:
8	chr20:25177243..25179011-chr20:25246862..25248615,2	K562	blood:
9	chr20:25175979..25179968-chr20:25200206..25203711,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction
ENSG00000101474	Chromatin interaction
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1007707	0.85[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs1007708	0.93[ASN][1000 genomes]
rs1044573	1.00[JPT][hapmap]
rs11087505	0.83[ASN][1000 genomes]
rs11100	1.00[JPT][hapmap]
rs1130694	1.00[JPT][hapmap]
rs11698185	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13038092	1.00[JPT][hapmap]
rs1473695	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.93[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	1.00[JPT][hapmap]
rs2261109	1.00[JPT][hapmap]
rs2261747	1.00[JPT][hapmap]
rs2261784	1.00[JPT][hapmap]
rs2268879	0.82[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2297496	1.00[JPT][hapmap]
rs2297497	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]
rs2500399	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	1.00[JPT][hapmap]
rs4813562	1.00[JPT][hapmap]
rs4815411	1.00[JPT][hapmap]
rs4815412	1.00[JPT][hapmap]
rs6037057	0.93[ASN][1000 genomes]
rs6037059	0.86[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[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6050426	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6050427	0.85[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6050429	0.93[ASN][1000 genomes]
rs6050431	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs6050432	0.93[ASN][1000 genomes]
rs6050439	0.93[ASN][1000 genomes]
rs6050442	0.93[ASN][1000 genomes]
rs6050445	0.83[ASN][1000 genomes]
rs6050477	0.86[JPT][hapmap]
rs6050513	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	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]
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	1.00[JPT][hapmap]
rs6107031	1.00[JPT][hapmap]
rs6115093	1.00[JPT][hapmap]
rs6115101	1.00[JPT][hapmap]
rs6115140	1.00[JPT][hapmap]
rs6115159	1.00[JPT][hapmap]
rs6132819	1.00[JPT][hapmap]
rs6138536	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6138537	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]
rs6138553	1.00[JPT][hapmap]
rs6138556	1.00[JPT][hapmap]
rs7020	1.00[JPT][hapmap]
rs7267979	1.00[JPT][hapmap]
rs7453	1.00[JPT][hapmap]
rs8115257	1.00[JPT][hapmap]
rs8124539	1.00[JPT][hapmap]
rs8184820	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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6050425	PYGB	cis	multi-tissue	Pritchard
rs6050425	ENTPD6	cis	parietal	SCAN
rs6050425	C20orf22	cis	multi-tissue	Pritchard
rs6050425	ABHD12	cis	lymphoblastoid	seeQTL
rs6050425	PYGB	cis	Whole Blood	GTEx
rs6050425	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs6050425	NINL	cis	parietal	SCAN
rs6050425	PYGB	cis	lymphoblastoid	seeQTL
rs6050425	NINL	cis	cerebellum	SCAN
rs6050425	CSTL1	cis	cerebellum	SCAN
rs6050425	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs6050425	ABHD12	cis	Nerve Tibial	GTEx
rs6050425	PYGB	cis	cerebellum	SCAN
rs6050425	ABHD12	cis	cerebellum	SCAN
rs6050425	HDHD4	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25175800-25178200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr20:25176600-25178200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr20:25176600-25178200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr20:25176600-25178200	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr20:25176800-25178200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr20:25177000-25178200	Flanking Active TSS	HMEC	breast
7	chr20:25177000-25178400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr20:25177000-25178400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr20:25177000-25178400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr20:25177000-25178400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr20:25177000-25178400	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr20:25177000-25178400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr20:25177000-25178600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr20:25177000-25178600	Flanking Active TSS	GM12878-XiMat	blood
15	chr20:25177000-25178800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr20:25177200-25178200	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr20:25177200-25178400	Enhancers	Small Intestine	intestine
18	chr20:25177200-25178600	Flanking Active TSS	Right Ventricle	heart
19	chr20:25177200-25178600	Enhancers	Spleen	Spleen
20	chr20:25177400-25178200	Flanking Active TSS	Pancreas	Pancrea
21	chr20:25177400-25178200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr20:25177400-25178400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr20:25177400-25178400	Flanking Active TSS	Colonic Mucosa	Colon
24	chr20:25177400-25178400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr20:25177400-25178600	Enhancers	Liver	Liver
26	chr20:25177400-25179400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr20:25177400-25179400	Weak transcription	HSMMtube	muscle
28	chr20:25177600-25178200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr20:25177600-25178200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:25177600-25178200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:25177600-25178200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr20:25177600-25178200	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr20:25177600-25178200	Flanking Active TSS	Left Ventricle	heart
34	chr20:25177600-25178200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr20:25177600-25178200	Enhancers	K562	blood
36	chr20:25177600-25178400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:25177600-25178400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr20:25177600-25178400	Enhancers	Primary B cells from peripheral blood	blood
39	chr20:25177600-25178400	Flanking Active TSS	Fetal Brain Female	brain
40	chr20:25177600-25178400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr20:25177600-25178400	Enhancers	Gastric	stomach
42	chr20:25177600-25178400	Enhancers	Lung	lung
43	chr20:25177600-25178400	Flanking Active TSS	Thymus	Thymus
44	chr20:25177600-25178400	Enhancers	Osteobl	bone
45	chr20:25177600-25178600	Enhancers	Adipose Nuclei	Adipose
46	chr20:25177600-25178600	Flanking Active TSS	Fetal Heart	heart
47	chr20:25177600-25178800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr20:25177600-25179600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr20:25177600-25179600	Weak transcription	NHDF-Ad	bronchial
50	chr20:25177600-25180800	Enhancers	Skeletal Muscle Male	skeletal muscle

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