Variant report

Variant	rs4774833
Chromosome Location	chr15:56210168-56210169
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	RCOR1	chr15:56209780-56210508	Hela-S3	cervix:	n/a	n/a
2	MAFK	chr15:56210053-56210781	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr15:56210140-56210290	AG09309	skin:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
4	CTCF	chr15:56210160-56210310	AG04449	skin:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
5	GATA3	chr15:56209986-56210542	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr15:56210160-56210310	HCPEpiC	choroid plexus:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
7	TBP	chr15:56210113-56210506	Hela-S3	cervix:	n/a	n/a
8	TCF12	chr15:56209915-56210618	A549	lung:	n/a	chr15:56209997-56210006
9	CTCF	chr15:56210075-56210383	HUVEC	blood vessel:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
10	CTCF	chr15:56210160-56210310	HBMEC	blood vessel:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
11	CTCF	chr15:56210140-56210290	HVMF	connective:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
12	CTCF	chr15:56210140-56210290	GM12878	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
13	CTCF	chr15:56210120-56210270	K562	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
14	CTCF	chr15:56210160-56210310	A549	lung:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
15	USF1	chr15:56210057-56210517	A549	lung:	n/a	n/a
16	CTCF	chr15:56210125-56210296	GM13977	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
17	CTCF	chr15:56210140-56210290	NHDF-neo	bronchial:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
18	RAD21	chr15:56209941-56210470	IMR90	lung:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
19	JUND	chr15:56210012-56210522	Hela-S3	cervix:	n/a	chr15:56210358-56210366
20	RAD21	chr15:56210014-56210438	HepG2	liver:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
21	CTCF	chr15:56210120-56210270	HMEC	breast:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
22	RAD21	chr15:56210088-56210406	H1-hESC	embryonic stem cell:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
23	SMC3	chr15:56209970-56210538	Hela-S3	cervix:	n/a	chr15:56210212-56210226 chr15:56210218-56210226
24	CTCF	chr15:56210140-56210290	HUVEC	blood vessel:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
25	RAD21	chr15:56210054-56210364	H1-hESC	embryonic stem cell:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
26	CTCF	chr15:56210156-56210278	MCF-7	breast:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
27	POLR2A	chr15:56210084-56210463	PANC-1	pancreas:	n/a	n/a
28	CTCF	chr15:56210080-56210230	GM12865	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
29	RAD21	chr15:56209996-56210478	MCF-7	breast:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
30	MYC	chr15:56210088-56210504	MCF10A-Er-Src	breast:	n/a	n/a
31	CTCF	chr15:56210140-56210290	Hela-S3	cervix:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
32	CTCF	chr15:56210040-56210190	RPTEC	kidney:	n/a	n/a
33	CTCF	chr15:56210100-56210250	HCM	heart:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
34	CTCF	chr15:56210160-56210310	BJ	skin:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
35	CTCF	chr15:56210080-56210230	GM12869	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
36	FOS	chr15:56210049-56210509	MCF10A-Er-Src	breast:	n/a	chr15:56210358-56210366
37	RAD21	chr15:56209929-56210544	A549	lung:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
38	GATA3	chr15:56210095-56210500	MCF-7	breast:	n/a	n/a
39	CTCF	chr15:56210141-56210273	Gliobla	brain:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
40	RAD21	chr15:56210088-56210271	HepG2	liver:	n/a	chr15:56210211-56210224 chr15:56210208-56210227
41	CTCF	chr15:56210128-56210313	Spleen_OC	spleen:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
42	CTCF	chr15:56209973-56210461	MCF-7	breast:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
43	NR3C1	chr15:56210114-56210521	A549	lung:	n/a	chr15:56210397-56210411 chr15:56210182-56210189
44	CTCF	chr15:56210120-56210270	HFF	foreskin:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
45	CTCF	chr15:56210042-56210366	A549	lung:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
46	CTCF	chr15:56210160-56210310	GM12871	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
47	CTCF	chr15:56210140-56210290	HCPEpiC	choroid plexus:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
48	CTCF	chr15:56210160-56210310	HPAF	blood vessel:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225
49	CTCF	chr15:56210040-56210190	HFF-Myc	foreskin:	n/a	n/a
50	CTCF	chr15:56210080-56210230	GM12801	blood:	n/a	chr15:56210210-56210228 chr15:56210216-56210225 chr15:56210212-56210225

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56209638..56212268-chr15:56534926..56537157,2	MCF-7	breast:
2	chr15:56189898..56190539-chr15:56209877..56210406,2	MCF-7	breast:

Variant related genes	Relation type
NEDD4	TF binding region
ENSG00000181827	Chromatin interaction
ENSG00000151575	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12442185	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819300	0.85[JPT][hapmap]
rs7174459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972348	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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 target site	22 gene(s)	inside rSNPs	diseases
3	nsv569542	chr15:56185262-56210929	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56176000-56216200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:56188600-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:56190000-56220000	Weak transcription	Pancreas	Pancrea
4	chr15:56190200-56221200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:56190400-56219800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:56200200-56213200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:56200800-56218000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
9	chr15:56201200-56217200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:56204800-56210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:56206800-56217800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:56207400-56210400	Weak transcription	Dnd41	blood
13	chr15:56207600-56210200	Flanking Active TSS	Osteobl	bone
14	chr15:56207600-56221200	Weak transcription	Right Ventricle	heart
15	chr15:56207800-56210600	Enhancers	HMEC	breast
16	chr15:56208200-56210400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:56208600-56210400	Enhancers	Rectal Smooth Muscle	rectum
18	chr15:56208600-56218000	Weak transcription	Esophagus	oesophagus
19	chr15:56208800-56221600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:56208800-56230000	Weak transcription	Liver	Liver
21	chr15:56209000-56210200	Flanking Active TSS	A549	lung
22	chr15:56209000-56218400	Weak transcription	Fetal Stomach	stomach
23	chr15:56209000-56230400	Weak transcription	Primary T cells from cord blood	blood
24	chr15:56209200-56210600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:56209200-56221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:56209200-56221600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:56209200-56230200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:56209200-56230200	Weak transcription	Aorta	Aorta
29	chr15:56209400-56210200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:56209400-56210200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:56209400-56210200	Enhancers	HSMMtube	muscle
32	chr15:56209400-56210400	Enhancers	HSMM	muscle
33	chr15:56209400-56210800	Enhancers	HUVEC	blood vessel
34	chr15:56209400-56210800	Enhancers	NHDF-Ad	bronchial
35	chr15:56209400-56211800	Enhancers	Hela-S3	cervix
36	chr15:56209600-56210200	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr15:56209600-56210800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:56209600-56210800	Enhancers	Stomach Mucosa	stomach
39	chr15:56209600-56211000	Enhancers	NHEK	skin
40	chr15:56209600-56216200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:56209600-56230800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:56209600-56247400	Weak transcription	Psoas Muscle	Psoas
43	chr15:56209800-56210400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr15:56209800-56211000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr15:56210000-56211000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:56210000-56211000	Enhancers	NHLF	lung
47	chr15:56210000-56216400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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