Variant report

Variant	rs1564509
Chromosome Location	chr4:1236562-1236563
allele	C/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	POLR2A	chr4:1234455-1238081	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:1236389-1237529	GM12892	blood:	n/a	n/a
3	TCF3	chr4:1236526-1237134	GM12878	blood:	n/a	n/a
4	NFATC1	chr4:1236386-1237099	GM12878	blood:	n/a	n/a
5	NFATC1	chr4:1236452-1237075	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:1236499-1237696	GM12878	blood:	n/a	n/a
7	STAT5A	chr4:1236499-1237084	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:1236520-1236888	GM12891	blood:	n/a	n/a
9	BCL3	chr4:1236545-1237132	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:1235978-1237744	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:1215883..1221793-chr4:1233494..1238232,6	K562	blood:
2	chr4:1210359..1211936-chr4:1235947..1237642,2	K562	blood:
3	chr4:1049115..1051492-chr4:1235735..1239693,3	MCF-7	breast:
4	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000163945	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11721789	0.88[EUR][1000 genomes]
rs11727987	0.87[EUR][1000 genomes]
rs12499546	0.88[EUR][1000 genomes]
rs12505362	0.87[EUR][1000 genomes]
rs12506095	0.87[EUR][1000 genomes]
rs12642797	0.88[EUR][1000 genomes]
rs13106092	0.88[EUR][1000 genomes]
rs13110563	0.88[EUR][1000 genomes]
rs13115355	0.87[EUR][1000 genomes]
rs13124444	0.86[EUR][1000 genomes]
rs13124876	0.88[EUR][1000 genomes]
rs13132584	0.88[EUR][1000 genomes]
rs13149790	0.87[EUR][1000 genomes]
rs1564508	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279281	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291199	0.88[EUR][1000 genomes]
rs2335855	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2878539	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3733338	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755924	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755927	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775092	0.87[EUR][1000 genomes]
rs3775094	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775099	0.80[EUR][1000 genomes]
rs3822017	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915420	0.87[EUR][1000 genomes]
rs4974541	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974542	0.88[EUR][1000 genomes]
rs4974543	0.88[EUR][1000 genomes]
rs4974544	0.88[EUR][1000 genomes]
rs4974577	0.84[EUR][1000 genomes]
rs4974578	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
6	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
13	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
17	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
19	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
21	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
22	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
23	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
24	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
26	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
27	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
28	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
29	esv1844406	chr4:1230397-1243775	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
30	esv1836927	chr4:1231363-1244037	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
31	esv1838677	chr4:1231540-1274734	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
32	nsv822433	chr4:1232688-1246206	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
33	nsv878334	chr4:1232910-1254930	Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1564509	UVSSA	cis	Thyroid	GTEx
rs1564509	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1564509	MAEA	cis	Nerve Tibial	GTEx
rs1564509	CTBP1-AS2	cis	Thyroid	GTEx
rs1564509	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1564509	UVSSA	cis	Whole Blood	GTEx
rs1564509	CTBP1	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
2	chr4:1212600-1237000	Strong transcription	Dnd41	blood
3	chr4:1214200-1236800	Strong transcription	Primary T cells from cord blood	blood
4	chr4:1214400-1238400	Strong transcription	Thymus	Thymus
5	chr4:1219000-1240200	Weak transcription	Hela-S3	cervix
6	chr4:1221600-1240200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:1222000-1240800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:1223000-1236600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:1223200-1236800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:1225000-1240200	Weak transcription	K562	blood
11	chr4:1227800-1236600	Strong transcription	Fetal Brain Female	brain
12	chr4:1228000-1236800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:1228400-1240000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:1228800-1238000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:1228800-1239400	Weak transcription	Fetal Brain Male	brain
16	chr4:1229000-1237000	Strong transcription	NHLF	lung
17	chr4:1229200-1240400	Weak transcription	Fetal Kidney	kidney
18	chr4:1229600-1237800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:1229600-1239600	Weak transcription	HSMM	muscle
20	chr4:1230000-1238200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:1230000-1240400	Weak transcription	HSMMtube	muscle
22	chr4:1231400-1236600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:1232000-1237200	Weak transcription	Primary B cells from cord blood	blood
24	chr4:1233400-1240600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:1234000-1238800	Weak transcription	NH-A	brain
26	chr4:1234200-1237400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:1234200-1239400	Weak transcription	Osteobl	bone
28	chr4:1234600-1237800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:1234600-1240400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:1234600-1240800	Genic enhancers	Spleen	Spleen
31	chr4:1234800-1237600	Weak transcription	NHDF-Ad	bronchial
32	chr4:1234800-1238800	Weak transcription	HMEC	breast
33	chr4:1234800-1240000	Genic enhancers	Fetal Intestine Large	intestine
34	chr4:1235000-1237000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:1235000-1237000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:1235000-1239800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:1235000-1240800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:1235000-1241200	Weak transcription	Aorta	Aorta
39	chr4:1235200-1236800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:1235200-1237000	Enhancers	Pancreas	Pancrea
41	chr4:1235200-1237600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr4:1235200-1237800	Genic enhancers	Fetal Intestine Small	intestine
43	chr4:1235200-1238000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:1235200-1238000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr4:1235200-1238200	Weak transcription	HepG2	liver
46	chr4:1235200-1238600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:1235200-1238600	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:1235200-1240000	Weak transcription	A549	lung
49	chr4:1235200-1240000	Weak transcription	HUVEC	blood vessel
50	chr4:1235200-1240200	Enhancers	Rectal Mucosa Donor 31	rectum

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