Variant report

Variant	rs4652355
Chromosome Location	chr1:179053051-179053052
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	chr1:179052925-179053061	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:179050421-179053208	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:179052905-179053349	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:179052705-179053172	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:179050072-179053327	GM19193	blood:	n/a	n/a
6	POLR2A	chr1:179049835-179053382	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:179052614-179053281	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:179049829-179053345	GM12878	blood:	n/a	n/a
9	ZNF143	chr1:179052780-179053070	GM12878	blood:	n/a	n/a
10	POU2F2	chr1:179052586-179053184	GM12878	blood:	n/a	chr1:179052872-179052890 chr1:179052873-179052888 chr1:179052876-179052887 chr1:179052892-179052904 chr1:179052877-179052884 chr1:179052891-179052904 chr1:179052949-179052970 chr1:179052877-179052885 chr1:179052851-179052866 chr1:179052895-179052902 chr1:179052874-179052886 chr1:179052875-179052885 chr1:179052891-179052906 chr1:179052874-179052888 chr1:179052876-179052885 chr1:179052894-179052903 chr1:179052873-179052886 chr1:179052875-179052885 chr1:179052893-179052903 chr1:179052893-179052903 chr1:179052876-179052886 chr1:179052892-179052906
11	CHD1	chr1:179052965-179053298	GM12878	blood:	n/a	n/a
12	POU2F2	chr1:179052645-179053073	GM12878	blood:	n/a	chr1:179052872-179052890 chr1:179052873-179052888 chr1:179052876-179052887 chr1:179052892-179052904 chr1:179052877-179052884 chr1:179052891-179052904 chr1:179052949-179052970 chr1:179052877-179052885 chr1:179052851-179052866 chr1:179052895-179052902 chr1:179052874-179052886 chr1:179052875-179052885 chr1:179052891-179052906 chr1:179052874-179052888 chr1:179052876-179052885 chr1:179052894-179052903 chr1:179052873-179052886 chr1:179052875-179052885 chr1:179052893-179052903 chr1:179052893-179052903 chr1:179052876-179052886 chr1:179052892-179052906
13	TBP	chr1:179052117-179053093	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:179050411-179053124	GM18505	blood:	n/a	n/a
15	RCOR1	chr1:179053017-179053203	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:179052941-179053316	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:179052673-179053403	GM12878	blood:	n/a	n/a
18	WRNIP1	chr1:179052785-179053179	GM12878	blood:	n/a	n/a
19	POU2F2	chr1:179052596-179053135	GM12891	blood:	n/a	chr1:179052872-179052890 chr1:179052873-179052888 chr1:179052876-179052887 chr1:179052892-179052904 chr1:179052877-179052884 chr1:179052891-179052904 chr1:179052949-179052970 chr1:179052877-179052885 chr1:179052851-179052866 chr1:179052895-179052902 chr1:179052874-179052886 chr1:179052875-179052885 chr1:179052891-179052906 chr1:179052874-179052888 chr1:179052876-179052885 chr1:179052894-179052903 chr1:179052873-179052886 chr1:179052875-179052885 chr1:179052893-179052903 chr1:179052893-179052903 chr1:179052876-179052886 chr1:179052892-179052906
20	POLR2A	chr1:179052945-179053309	HepG2	liver:	n/a	n/a
21	BHLHE40	chr1:179052947-179053073	K562	blood:	n/a	n/a
22	RELA	chr1:179051858-179053199	GM19099	blood:	n/a	n/a
23	POLR2A	chr1:179050051-179053211	Raji	blood:	n/a	n/a
24	POU2F2	chr1:179052678-179053128	GM12891	blood:	n/a	chr1:179052872-179052890 chr1:179052873-179052888 chr1:179052876-179052887 chr1:179052892-179052904 chr1:179052877-179052884 chr1:179052891-179052904 chr1:179052949-179052970 chr1:179052877-179052885 chr1:179052851-179052866 chr1:179052895-179052902 chr1:179052874-179052886 chr1:179052875-179052885 chr1:179052891-179052906 chr1:179052874-179052888 chr1:179052876-179052885 chr1:179052894-179052903 chr1:179052873-179052886 chr1:179052875-179052885 chr1:179052893-179052903 chr1:179052893-179052903 chr1:179052876-179052886 chr1:179052892-179052906

No.	Distal block	Cell Line	Cell type
1	chr1:178903732..178906494-chr1:179051387..179053146,2	K562	blood:
2	chr1:179051673..179054487-chr1:179062645..179065575,2	K562	blood:
3	chr1:179051978..179053865-chr1:179066668..179068883,2	K562	blood:
4	chr1:179050855..179053575-chr1:179263211..179266215,3	K562	blood:
5	chr1:179051431..179053361-chr1:179162011..179164683,2	MCF-7	breast:
6	chr1:179049424..179053663-chr1:179259743..179264339,5	MCF-7	breast:
7	chr1:178994647..178996585-chr1:179051040..179053373,3	MCF-7	breast:

Variant related genes	Relation type
TOR3A	TF binding region
ENSG00000116199	Chromatin interaction
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10913673	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs10913689	0.84[JPT][hapmap]
rs1128952	0.84[JPT][hapmap];0.81[MKK][hapmap]
rs12041914	0.93[ASN][1000 genomes]
rs12064702	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12733622	0.89[JPT][hapmap]
rs12735672	0.88[JPT][hapmap]
rs2274227	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766636	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs4652350	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs4652352	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs7517000	0.81[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7517999	0.89[JPT][hapmap]
rs7548966	0.88[CHD][hapmap];0.89[JPT][hapmap]
rs9659206	0.81[AFR][1000 genomes]
rs9729556	0.81[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4652355	FAM20B	cis	multi-tissue	Pritchard
rs4652355	FAM20B	cis	parietal	SCAN
rs4652355	FAM20B	cis	lymphoblastoid	seeQTL
rs4652355	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179052000-179053400	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr1:179052200-179053200	Enhancers	Spleen	Spleen
3	chr1:179052200-179053400	Enhancers	Stomach Mucosa	stomach
4	chr1:179052200-179062200	Weak transcription	Small Intestine	intestine
5	chr1:179052400-179053200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:179052400-179053200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:179052400-179053200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:179052400-179053200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:179052400-179053200	Enhancers	Brain Hippocampus Middle	brain
10	chr1:179052400-179053200	Enhancers	Fetal Intestine Large	intestine
11	chr1:179052400-179053200	Enhancers	Fetal Intestine Small	intestine
12	chr1:179052400-179053200	Enhancers	Pancreas	Pancrea
13	chr1:179052400-179053200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr1:179052400-179053400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:179052400-179053400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:179052400-179053800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:179052400-179053800	Weak transcription	Brain Anterior Caudate	brain
18	chr1:179052400-179053800	Weak transcription	Colonic Mucosa	Colon
19	chr1:179052400-179053800	Weak transcription	Gastric	stomach
20	chr1:179052400-179053800	Weak transcription	Lung	lung
21	chr1:179052400-179053800	Weak transcription	Ovary	ovary
22	chr1:179052400-179053800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:179052400-179054400	Weak transcription	Right Ventricle	heart
24	chr1:179052400-179054600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:179052400-179054800	Weak transcription	Aorta	Aorta
26	chr1:179052400-179054800	Weak transcription	Brain Germinal Matrix	brain
27	chr1:179052400-179054800	Weak transcription	Brain Substantia Nigra	brain
28	chr1:179052400-179054800	Weak transcription	Left Ventricle	heart
29	chr1:179052400-179054800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:179052400-179054800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:179052400-179056000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:179052400-179056000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:179052400-179056200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:179052400-179056400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:179052400-179056600	Weak transcription	Right Atrium	heart
36	chr1:179052400-179056600	Weak transcription	HUVEC	blood vessel
37	chr1:179052400-179058800	Weak transcription	NH-A	brain
38	chr1:179052400-179059000	Weak transcription	Psoas Muscle	Psoas
39	chr1:179052400-179060000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:179052400-179060200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:179052400-179060800	Weak transcription	Fetal Lung	lung
42	chr1:179052400-179062600	Weak transcription	Fetal Kidney	kidney
43	chr1:179052600-179053200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:179052600-179053200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:179052600-179053200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:179052600-179053400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:179052600-179053400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:179052600-179053400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:179052600-179053400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr1:179052600-179053600	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links