Variant report

Variant	rs4683326
Chromosome Location	chr3:47292827-47292828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47292810..47293742-chr3:47411913..47413200,3	K562	blood:
2	chr3:47292029..47293531-chr8:33370667..33372185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129696	Chromatin interaction
ENSG00000239039	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap]
rs1076394	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap]
rs11130115	0.88[CEU][hapmap]
rs11130123	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130126	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11130128	0.96[CEU][hapmap]
rs11130129	0.96[CEU][hapmap]
rs11705957	0.96[CEU][hapmap]
rs11710013	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11710121	0.87[CEU][hapmap]
rs11710322	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11711824	0.95[CEU][hapmap]
rs11712445	0.95[CEU][hapmap]
rs11714294	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11719877	0.96[CEU][hapmap]
rs11915074	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11921117	0.89[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap]
rs13061071	0.88[CEU][hapmap]
rs13072802	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075233	0.96[CEU][hapmap]
rs13094438	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1531875	0.96[CEU][hapmap]
rs1638676	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17410853	0.87[CEU][hapmap]
rs17411375	1.00[CEU][hapmap]
rs17476234	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap]
rs2088135	0.81[EUR][1000 genomes]
rs2132173	0.88[CEU][hapmap];0.80[ASN][1000 genomes]
rs2159400	1.00[CEU][hapmap]
rs2276853	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs295428	1.00[CEU][hapmap]
rs295441	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295449	1.00[CEU][hapmap]
rs295458	1.00[CEU][hapmap]
rs295461	1.00[CEU][hapmap]
rs3736177	0.95[CEU][hapmap]
rs4078466	0.84[CEU][hapmap];0.95[YRI][hapmap]
rs4082155	0.84[CEU][hapmap]
rs4682852	0.89[CEU][hapmap];0.96[YRI][hapmap]
rs4683324	0.80[ASN][1000 genomes]
rs4858811	0.96[CEU][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.96[CEU][hapmap]
rs4858893	0.96[CEU][hapmap]
rs4858894	0.87[CEU][hapmap]
rs56250009	0.81[EUR][1000 genomes]
rs59689369	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6768221	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap]
rs6780013	0.87[CEU][hapmap]
rs6791842	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap]
rs6800271	0.96[CEU][hapmap]
rs7632501	0.81[EUR][1000 genomes]
rs7636423	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap]
rs807932	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs807935	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs807936	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs807937	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs811115	0.95[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap]
rs9683033	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4683326	RTP3	cis	lesional skin	skin_eQTL
rs4683326	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs4683326	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:47277600-47300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:47282200-47300400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:47282200-47300600	Weak transcription	Lung	lung
9	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:47283400-47293200	Weak transcription	Psoas Muscle	Psoas
11	chr3:47284800-47300400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
13	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:47286400-47299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:47287200-47293200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:47287400-47299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:47291000-47293000	Enhancers	Liver	Liver
18	chr3:47291800-47293600	Enhancers	HepG2	liver
19	chr3:47292000-47293400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:47292000-47293400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:47292000-47293600	Enhancers	K562	blood
22	chr3:47292400-47293600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:47292600-47293600	Enhancers	Spleen	Spleen

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