Variant report

Variant	rs16890561
Chromosome Location	chr6:38297788-38297789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10484927	0.89[ASW][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10484930	0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs11964070	0.81[AMR][1000 genomes]
rs12055513	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12524225	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12527432	1.00[ASW][hapmap];0.84[CHD][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs12529549	0.83[ASN][1000 genomes]
rs12660323	0.86[CHD][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs12664994	0.81[JPT][hapmap]
rs16890552	0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs16890588	0.81[AMR][1000 genomes]
rs2395697	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711531	0.86[CHD][hapmap];1.00[TSI][hapmap]
rs4714139	0.86[CHD][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap]
rs4714145	0.85[JPT][hapmap];0.90[YRI][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57012325	0.82[ASN][1000 genomes]
rs57575973	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57934228	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs59459724	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60500173	0.82[ASN][1000 genomes]
rs6917308	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6938840	0.82[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs714930	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73422824	0.85[ASN][1000 genomes]
rs73422833	0.85[ASN][1000 genomes]
rs73730928	0.80[ASN][1000 genomes]
rs764347	0.85[ASN][1000 genomes]
rs7771835	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs871182	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs871184	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs9296243	1.00[ASW][hapmap];1.00[TSI][hapmap]
rs9349065	0.86[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs9349069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349071	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349074	0.81[AMR][1000 genomes]
rs9357268	0.81[AMR][1000 genomes]
rs9366956	1.00[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369046	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9369047	1.00[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9369050	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9369052	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369053	0.81[AMR][1000 genomes]
rs9380728	0.82[YRI][hapmap]
rs9380734	0.84[ASN][1000 genomes]
rs9380735	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380736	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380738	0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs9380744	0.89[ASW][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9394487	0.89[ASW][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs9394490	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9394491	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9394496	0.89[ASW][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active 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 target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38275400-38301200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:38278000-38310600	Weak transcription	Gastric	stomach
3	chr6:38278400-38305400	Weak transcription	Pancreas	Pancrea
4	chr6:38282600-38301400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:38283000-38304000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:38284800-38301200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:38287400-38301200	Weak transcription	Primary B cells from cord blood	blood
9	chr6:38287600-38301200	Weak transcription	Primary T cells from cord blood	blood
10	chr6:38288000-38305600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:38289200-38301000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:38291000-38305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:38291400-38317600	Weak transcription	Rectal Smooth Muscle	rectum

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