Variant report

Variant	rs295442
Chromosome Location	chr3:47335881-47335882
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47334914..47337230-chr3:47365085..47366632,2	MCF-7	breast:
2	chr3:47330452..47333849-chr3:47334869..47338744,4	MCF-7	breast:
3	chr3:47203167..47206119-chr3:47335033..47336755,2	K562	blood:

Variant related genes	Relation type
ENSG00000227398	Chromatin interaction
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs1076394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap]
rs11130115	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs11130123	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130126	0.92[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11705957	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs11710013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710121	0.85[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711824	0.96[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs11712445	0.96[CEU][hapmap]
rs11714294	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11719877	0.96[CEU][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs11915074	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11921117	0.84[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs13061071	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs13072802	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs13094438	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1531875	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs1638676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs17476234	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs2101247	0.92[CEU][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs2132173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs295458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs295461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs3736177	0.96[CEU][hapmap]
rs4682852	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.96[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs59689369	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767907	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs6768221	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs6800271	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs7636423	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807935	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807937	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878659	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap]
rs9683033	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs9837343	0.81[CEU][hapmap];0.89[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs295442	C3orf75	cis	cerebellum	SCAN
rs295442	AMIGO3	cis	cerebellum	SCAN
rs295442	CCDC12	cis	cerebellum	SCAN
rs295442	SCAP	cis	parietal	SCAN
rs295442	CCHCR1	trans	lymphoblastoid	seeQTL
rs295442	RTP3	cis	lesional skin	skin_eQTL
rs295442	PRKAR2A	cis	cerebellum	SCAN
rs295442	HYAL2	cis	cerebellum	SCAN
rs295442	NCKIPSD	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47325600-47337800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:47325600-47338000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:47325600-47344600	Weak transcription	Ovary	ovary
5	chr3:47325600-47367600	Weak transcription	A549	lung
6	chr3:47325800-47337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:47325800-47338000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:47325800-47338200	Weak transcription	HUVEC	blood vessel
9	chr3:47325800-47343800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:47325800-47352000	Weak transcription	Fetal Kidney	kidney
11	chr3:47326200-47336400	Weak transcription	Lung	lung
12	chr3:47326200-47340800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:47326200-47344600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:47326200-47356200	Weak transcription	Fetal Heart	heart
15	chr3:47326200-47356600	Weak transcription	NHDF-Ad	bronchial
16	chr3:47326200-47359600	Weak transcription	Fetal Lung	lung
17	chr3:47326200-47362200	Weak transcription	Gastric	stomach
18	chr3:47326200-47363200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:47326400-47338200	Weak transcription	Stomach Mucosa	stomach
20	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:47326600-47341200	Weak transcription	Placenta	Placenta
22	chr3:47326600-47351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:47326800-47356600	Weak transcription	Small Intestine	intestine
24	chr3:47327000-47344400	Weak transcription	Brain Angular Gyrus	brain
25	chr3:47327200-47336600	Strong transcription	Primary T cells from cord blood	blood
26	chr3:47327600-47348400	Weak transcription	Fetal Brain Male	brain
27	chr3:47328400-47364400	Weak transcription	Pancreas	Pancrea
28	chr3:47328600-47336600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:47328600-47338400	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:47328800-47336800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:47329200-47359800	Weak transcription	NHLF	lung
32	chr3:47329600-47340800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:47330000-47343400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:47330400-47337400	Weak transcription	Spleen	Spleen
35	chr3:47330400-47352000	Weak transcription	NHEK	skin
36	chr3:47330400-47356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:47330600-47336200	Weak transcription	Brain Anterior Caudate	brain
38	chr3:47330600-47346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:47330600-47359800	Weak transcription	Hela-S3	cervix
40	chr3:47330600-47360600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:47330800-47337600	Weak transcription	Colonic Mucosa	Colon
42	chr3:47330800-47344200	Weak transcription	HSMMtube	muscle
43	chr3:47330800-47356600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:47330800-47361800	Weak transcription	HMEC	breast
45	chr3:47331000-47344000	Weak transcription	HSMM	muscle
46	chr3:47331200-47337000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:47331200-47344000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:47331400-47337800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:47331400-47343200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:47331400-47343400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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