Variant report

Variant	rs1961996
Chromosome Location	chr8:120139895-120139896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1156545	0.89[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs1158945	0.82[JPT][hapmap]
rs11994775	0.82[JPT][hapmap]
rs12542116	0.86[YRI][hapmap]
rs13248274	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13248569	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13257113	0.92[ASN][1000 genomes]
rs13262749	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1351952	0.82[JPT][hapmap]
rs1351954	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1364709	0.85[CEU][hapmap]
rs1385492	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1385493	0.85[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs1385496	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1385498	0.81[CEU][hapmap]
rs1425055	0.85[CEU][hapmap]
rs1485293	0.82[JPT][hapmap]
rs1872424	0.81[CEU][hapmap]
rs1905775	0.86[CHD][hapmap]
rs2113885	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242313	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247769	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2432965	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450061	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2450065	0.82[JPT][hapmap]
rs2450067	0.82[JPT][hapmap]
rs2450068	0.82[JPT][hapmap]
rs2450069	0.82[JPT][hapmap]
rs2450072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450080	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465383	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs2465385	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465387	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465390	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465392	0.82[JPT][hapmap]
rs2465393	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465394	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2465395	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465403	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs2465404	0.82[JPT][hapmap]
rs2468177	0.85[CEU][hapmap]
rs2468181	0.85[CEU][hapmap]
rs2468182	0.85[CEU][hapmap]
rs6469811	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6994271	0.92[ASN][1000 genomes]
rs7388447	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7813952	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7827224	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs996789	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1804892	chr8:120120429-120161140	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv1810588	chr8:120120429-120168446	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1808446	chr8:120120901-120168446	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1812136	chr8:120127586-120161140	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1810758	chr8:120135125-120161140	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1814238	chr8:120135125-120161140	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv612062	chr8:120135125-120161140	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv3416446	chr8:120139571-120141469	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1961996	SAMD12	cis	parietal	SCAN
rs1961996	NOV	cis	cerebellum	SCAN
rs1961996	MAL2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120134800-120141600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:120134800-120141600	Weak transcription	NHEK	skin
3	chr8:120134800-120141800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:120134800-120147600	Weak transcription	HMEC	breast
5	chr8:120136600-120141600	Weak transcription	H9 Cell Line	embryonic stem cell

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