Variant report

Variant	rs6764042
Chromosome Location	chr3:46059139-46059140
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	chr3:46058613..46061881-chr3:46065109..46067652,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XCR1-1	chr3:46058516-46062157	NONHSAT089426

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11130080	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11130085	0.83[ASN][1000 genomes]
rs11130086	0.82[ASN][1000 genomes]
rs11917890	0.83[ASN][1000 genomes]
rs11929281	0.83[ASN][1000 genomes]
rs12485978	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs12495073	0.96[ASN][1000 genomes]
rs12496322	0.83[ASN][1000 genomes]
rs12629632	0.83[EUR][1000 genomes]
rs12630101	0.95[JPT][hapmap]
rs12635657	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12637023	0.83[ASN][1000 genomes]
rs12639598	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs13059919	0.90[ASN][1000 genomes]
rs13060901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065737	0.83[EUR][1000 genomes]
rs13073861	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs13077099	0.83[ASN][1000 genomes]
rs13078053	0.80[ASN][1000 genomes]
rs13082280	0.82[EUR][1000 genomes]
rs13098271	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13434029	0.82[EUR][1000 genomes]
rs13434336	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1392290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1491959	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1500005	0.91[ASN][1000 genomes]
rs1546077	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs1602579	0.83[EUR][1000 genomes]
rs1604069	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17078495	0.83[ASN][1000 genomes]
rs17078577	0.83[ASN][1000 genomes]
rs1909595	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1909596	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1976366	0.81[EUR][1000 genomes]
rs1976367	0.85[EUR][1000 genomes]
rs1994490	0.95[JPT][hapmap]
rs2036292	0.90[ASN][1000 genomes]
rs2131091	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs2201984	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373151	0.82[EUR][1000 genomes]
rs2373154	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs28808964	0.91[ASN][1000 genomes]
rs34381514	0.91[ASN][1000 genomes]
rs34906043	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35359253	0.83[EUR][1000 genomes]
rs35435608	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35462017	0.83[EUR][1000 genomes]
rs35537559	0.83[ASN][1000 genomes]
rs35567508	0.80[ASN][1000 genomes]
rs35657218	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35688834	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733100	0.95[JPT][hapmap]
rs3796375	0.95[JPT][hapmap]
rs3821884	0.95[JPT][hapmap]
rs3851347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4234452	0.91[ASN][1000 genomes]
rs4314213	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4333119	0.91[ASN][1000 genomes]
rs4490402	0.82[JPT][hapmap]
rs4682806	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682810	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4683168	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683175	0.83[ASN][1000 genomes]
rs4683178	0.83[ASN][1000 genomes]
rs59226168	0.83[ASN][1000 genomes]
rs59521415	0.83[EUR][1000 genomes]
rs60539039	0.93[ASN][1000 genomes]
rs62242796	0.83[ASN][1000 genomes]
rs67044455	0.83[ASN][1000 genomes]
rs6778896	0.83[ASN][1000 genomes]
rs6780163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs6784214	0.88[CEU][hapmap]
rs6794103	0.83[ASN][1000 genomes]
rs6795629	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs6800484	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6805094	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809381	0.88[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs730983	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs737452	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs751552	0.95[JPT][hapmap]
rs751553	0.95[JPT][hapmap]
rs7609756	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7610518	0.83[EUR][1000 genomes]
rs7616464	0.91[ASN][1000 genomes]
rs7623190	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7623460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623476	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs7631598	0.90[ASN][1000 genomes]
rs7642701	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643426	0.85[CHB][hapmap]
rs9311386	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9311387	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs931704	0.83[ASN][1000 genomes]
rs9637425	0.84[ASN][1000 genomes]
rs9824886	0.90[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9849015	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9863204	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870445	0.84[ASN][1000 genomes]
rs9876587	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9990063	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46037600-46064600	Weak transcription	Gastric	stomach
2	chr3:46055200-46060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:46055400-46060800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:46058800-46059800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:46058800-46060200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:46059000-46059200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:46059000-46059600	Enhancers	GM12878-XiMat	blood
8	chr3:46059000-46059800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:46059000-46059800	Enhancers	HSMMtube	muscle
10	chr3:46059000-46060000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:46059000-46060000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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