Variant report

Variant	rs2621306
Chromosome Location	chr3:158977434-158977435
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158837926..158840108-chr3:158976844..158979055,2	K562	blood:
2	chr3:158563458..158564296-chr3:158976821..158978499,10	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1020470	0.84[YRI][hapmap]
rs12635142	0.87[CHB][hapmap]
rs13074822	0.83[CHB][hapmap]
rs1375403	0.83[CHB][hapmap]
rs1375405	0.83[CHB][hapmap]
rs1375407	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1448998	0.83[CHB][hapmap]
rs1449009	0.89[YRI][hapmap]
rs1449012	0.83[CHB][hapmap]
rs1449024	0.83[CHB][hapmap]
rs1449027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1562671	0.83[CHB][hapmap]
rs1562672	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs17795566	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1900861	0.82[CHB][hapmap]
rs1975601	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2084507	0.83[CHB][hapmap];0.85[GIH][hapmap]
rs2365478	0.91[CHB][hapmap]
rs2595232	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2595236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2595238	0.99[ASN][1000 genomes]
rs2595239	0.97[ASN][1000 genomes]
rs2595242	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2595243	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2595244	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs2595245	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2595246	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs2595247	0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs2595248	0.95[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2595250	0.89[ASN][1000 genomes]
rs2595258	0.87[CHB][hapmap];0.86[CHD][hapmap]
rs2595263	0.84[ASN][1000 genomes]
rs2621277	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs2621282	0.96[ASN][1000 genomes]
rs2621284	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2621290	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2621292	0.87[CHB][hapmap]
rs2621294	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2621295	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2621297	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs2621299	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2621300	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2621305	0.88[YRI][hapmap]
rs2621310	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2621312	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs2621313	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2621314	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2922407	0.85[YRI][hapmap]
rs35192832	0.98[ASN][1000 genomes]
rs3903320	0.86[YRI][hapmap]
rs4645169	0.91[CHB][hapmap]
rs4680494	0.90[CHB][hapmap]
rs4680495	0.91[CHB][hapmap]
rs4680500	0.83[CHB][hapmap]
rs6441255	0.83[CHB][hapmap]
rs6787941	0.83[CHB][hapmap];0.85[GIH][hapmap]
rs6789496	0.82[CHB][hapmap]
rs6807076	0.83[CHB][hapmap]
rs73166218	0.96[ASN][1000 genomes]
rs7428369	0.83[CHB][hapmap]
rs7624604	0.86[YRI][hapmap]
rs7634829	0.82[CHB][hapmap]
rs7646959	0.83[CHB][hapmap]
rs9879667	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3426016	chr3:158676623-158979242	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2621306	IQCJ	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158972200-158977800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:158977000-158983000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links