Variant report

Variant	rs6138475
Chromosome Location	chr20:25013357-25013358
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	TBP	chr20:25013317-25013882	HepG2	liver:	n/a	n/a
2	TCF7L2	chr20:25013276-25013843	HepG2	liver:	n/a	chr20:25013316-25013325 chr20:25013317-25013324
3	NFIC	chr20:25013088-25014137	HepG2	liver:	n/a	chr20:25014109-25014125 chr20:25014108-25014125
4	REST	chr20:25013259-25013674	HepG2	liver:	n/a	n/a
5	E2F6	chr20:25012632-25013672	H1-hESC	embryonic stem cell:	n/a	chr20:25013603-25013610 chr20:25013599-25013606
6	ZBTB7A	chr20:25013068-25013475	HepG2	liver:	n/a	chr20:25013227-25013236
7	RAD21	chr20:25013261-25013765	HepG2	liver:	n/a	n/a
8	HDAC2	chr20:25012846-25014134	HepG2	liver:	n/a	n/a
9	MAX	chr20:25012833-25013800	H1-hESC	embryonic stem cell:	n/a	n/a
10	HDAC2	chr20:25013053-25013795	HepG2	liver:	n/a	n/a
11	EP300	chr20:25013030-25013771	HepG2	liver:	n/a	chr20:25013296-25013306
12	MAX	chr20:25012665-25013823	HepG2	liver:	n/a	chr20:25012771-25012781
13	RAD21	chr20:25013268-25013828	HepG2	liver:	n/a	n/a
14	RCOR1	chr20:25013274-25013628	HepG2	liver:	n/a	n/a
15	HNF4G	chr20:25013127-25013652	HepG2	liver:	n/a	chr20:25013224-25013246
16	MYBL2	chr20:25012955-25014078	HepG2	liver:	n/a	n/a
17	RFX5	chr20:25013340-25013777	HepG2	liver:	n/a	n/a
18	RAD21	chr20:25013350-25013944	HepG2	liver:	n/a	n/a
19	EGR1	chr20:25013344-25013791	H1-hESC	embryonic stem cell:	n/a	chr20:25013619-25013634 chr20:25013620-25013633 chr20:25013621-25013632 chr20:25013620-25013633 chr20:25013620-25013633 chr20:25013621-25013631 chr20:25013621-25013630 chr20:25013620-25013633 chr20:25013621-25013631 chr20:25013622-25013631 chr20:25013619-25013633 chr20:25013621-25013632
20	MAX	chr20:25012785-25013674	HepG2	liver:	n/a	n/a
21	FOXA2	chr20:25013150-25013663	HepG2	liver:	n/a	n/a
22	YY1	chr20:25013142-25013789	HepG2	liver:	n/a	n/a
23	FOXA1	chr20:25013078-25013562	HepG2	liver:	n/a	n/a
24	HEY1	chr20:25013169-25013890	HepG2	liver:	n/a	n/a
25	FOXA1	chr20:25013043-25013508	HepG2	liver:	n/a	n/a
26	EP300	chr20:25012975-25013907	HepG2	liver:	n/a	chr20:25013296-25013306
27	MYBL2	chr20:25013040-25013687	HepG2	liver:	n/a	n/a
28	MAX	chr20:25012780-25013673	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPD	chr20:25013114-25013908	HepG2	liver:	n/a	n/a
30	ZBTB7A	chr20:25013025-25013447	HepG2	liver:	n/a	chr20:25013227-25013236
31	FOXA1	chr20:25013127-25013600	HepG2	liver:	n/a	n/a
32	POLR2A	chr20:25013328-25013936	HepG2	liver:	n/a	n/a
33	EP300	chr20:25013098-25013820	HepG2	liver:	n/a	chr20:25013296-25013306
34	POLR2A	chr20:25013320-25013885	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ACSS1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1007881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1056036	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs11700073	0.86[JPT][hapmap]
rs11905625	0.86[JPT][hapmap]
rs1535042	0.86[JPT][hapmap]
rs2008275	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs2179732	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs227625	0.86[JPT][hapmap]
rs227633	0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs227634	0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs227650	0.85[JPT][hapmap]
rs227653	0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs3746330	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs41315094	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4815351	0.86[JPT][hapmap]
rs4815357	0.86[JPT][hapmap]
rs6037010	0.87[ASN][1000 genomes]
rs6050201	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050249	0.82[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs6050255	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6050259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6050261	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6050263	0.87[ASN][1000 genomes]
rs6083699	0.86[JPT][hapmap]
rs6083709	0.86[JPT][hapmap]
rs60849220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114980	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6114981	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6114984	0.84[JPT][hapmap]
rs6132775	0.83[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs6132777	0.83[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs6132778	0.86[JPT][hapmap]
rs6132784	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6132788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6132790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6138437	0.86[JPT][hapmap]
rs6138442	0.86[JPT][hapmap]
rs6138453	0.86[JPT][hapmap]
rs6138455	0.86[JPT][hapmap]
rs6138457	0.86[JPT][hapmap]
rs6138458	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138464	0.85[EUR][1000 genomes]
rs6138465	0.88[EUR][1000 genomes]
rs6138466	0.82[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6138473	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6138474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs62217173	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62217174	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62217175	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6707	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs7268095	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs7273518	0.84[ASN][1000 genomes]
rs8125909	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs8183891	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24988200-25016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:24995800-25016400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr20:24997200-25016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr20:24997400-25016400	Weak transcription	GM12878-XiMat	blood
5	chr20:24998600-25016600	Weak transcription	Liver	Liver
6	chr20:24999800-25016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr20:25002000-25013800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr20:25004800-25016600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr20:25007600-25014000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:25007800-25013400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr20:25007800-25014800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr20:25008600-25013800	Weak transcription	Fetal Kidney	kidney
13	chr20:25009200-25014000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr20:25009200-25016600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr20:25010000-25017800	Weak transcription	NHDF-Ad	bronchial
16	chr20:25010200-25015000	Strong transcription	Primary T cells from cord blood	blood
17	chr20:25010600-25014800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr20:25011200-25014800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr20:25011200-25015200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr20:25011400-25014800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr20:25011400-25016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr20:25011600-25013400	Genic enhancers	Fetal Intestine Large	intestine
23	chr20:25011600-25013400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr20:25011600-25013600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr20:25011600-25013800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr20:25011600-25015000	Genic enhancers	Fetal Intestine Small	intestine
27	chr20:25011600-25015000	Enhancers	Left Ventricle	heart
28	chr20:25011600-25015600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr20:25011600-25016200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr20:25011600-25016400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr20:25011600-25016400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr20:25011600-25016800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr20:25011600-25017800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr20:25011600-25017800	Enhancers	Placenta	Placenta
35	chr20:25011600-25020200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr20:25011800-25016800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr20:25012000-25013400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr20:25012000-25016400	Weak transcription	Thymus	Thymus
39	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
40	chr20:25012200-25013400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:25012200-25015000	Enhancers	Fetal Heart	heart
42	chr20:25012200-25015200	Enhancers	Fetal Muscle Leg	muscle
43	chr20:25012400-25014600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:25012400-25014600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:25012400-25014600	Enhancers	Fetal Brain Male	brain
46	chr20:25012400-25014600	Enhancers	Ovary	ovary
47	chr20:25012400-25015000	Genic enhancers	Fetal Stomach	stomach
48	chr20:25012400-25015200	Enhancers	Stomach Mucosa	stomach
49	chr20:25012400-25016400	Weak transcription	Dnd41	blood
50	chr20:25012600-25013400	Weak transcription	Primary B cells from cord blood	blood

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