Variant report

Variant	rs2028988
Chromosome Location	chr3:160686436-160686437
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160683839..160685876-chr3:160685916..160688095,2	K562	blood:
2	chr3:160685063..160687568-chr3:161087715..161090731,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10513558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10513560	0.81[JPT][hapmap]
rs11709802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494673	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs12496196	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12498008	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12635022	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12696110	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs13079358	0.90[CEU][hapmap]
rs13079792	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13086445	0.90[EUR][1000 genomes]
rs13325518	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1348977	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs1374786	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1374795	0.81[CHD][hapmap]
rs1447608	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1447617	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs1447624	0.86[JPT][hapmap]
rs1530635	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1530636	0.81[JPT][hapmap]
rs1562465	0.81[JPT][hapmap]
rs1562466	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1599382	0.86[JPT][hapmap]
rs16831758	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1839020	0.90[EUR][1000 genomes]
rs1868104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1868106	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs1971240	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2061580	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs2121721	0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4608736	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4679667	1.00[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs4679925	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679927	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60875417	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6441334	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6441336	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6441342	0.90[EUR][1000 genomes]
rs6441343	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441344	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441345	0.81[JPT][hapmap]
rs6770488	0.93[JPT][hapmap]
rs6776120	0.85[JPT][hapmap]
rs6785844	1.00[CEU][hapmap]
rs6787694	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6789195	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6797498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798966	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6799391	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs6800013	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808386	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7610732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7613316	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7616249	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs7617759	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs7619552	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629001	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7635796	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7640874	0.86[JPT][hapmap]
rs7644586	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7653744	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778644	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs778647	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs778650	0.91[ASW][hapmap];0.84[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs778651	0.81[JPT][hapmap]
rs778652	0.86[JPT][hapmap]
rs778655	0.93[JPT][hapmap]
rs796610	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs814092	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs878954	0.94[EUR][1000 genomes]
rs878955	0.92[EUR][1000 genomes]
rs898676	0.86[JPT][hapmap]
rs935500	0.90[EUR][1000 genomes]
rs9813700	0.88[ASN][1000 genomes]
rs9814174	1.00[CEU][hapmap]
rs9818081	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9850546	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9857743	0.86[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv592135	chr3:160682500-160689164	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160667400-160696000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:160670200-160686600	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:160678400-160697600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:160679000-160686600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:160681000-160686600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:160682400-160686600	Weak transcription	Left Ventricle	heart
8	chr3:160683800-160687000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:160684600-160689200	Weak transcription	Dnd41	blood
10	chr3:160685200-160686800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:160685400-160686800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:160685400-160687000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:160686400-160687000	Enhancers	Psoas Muscle	Psoas
14	chr3:160686400-160687200	Enhancers	Skeletal Muscle Male	skeletal muscle

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