Variant report

Variant	rs13248274
Chromosome Location	chr8:120163391-120163392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1156545	0.89[CEU][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs1158945	0.82[JPT][hapmap]
rs11994775	0.82[JPT][hapmap]
rs12542116	1.00[YRI][hapmap]
rs13248569	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13257113	0.97[ASN][1000 genomes]
rs13262749	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1351952	0.82[JPT][hapmap]
rs1351954	0.88[ASN][1000 genomes]
rs1364709	0.85[CEU][hapmap]
rs1385492	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1385493	0.85[CEU][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs1385496	0.89[CEU][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]
rs1961996	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113885	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242313	0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2247769	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs2432965	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450061	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450076	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450080	0.82[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2465383	0.89[CEU][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs2465385	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2465387	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465390	0.95[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465392	0.82[JPT][hapmap]
rs2465393	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465394	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465403	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	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6994271	0.97[ASN][1000 genomes]
rs7388447	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7813952	0.96[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7827224	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs996789	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
5	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
6	nsv6363	chr8:120150231-120188957	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3584893	chr8:120154784-120163755	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv612073	chr8:120155591-120165257	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv612074	chr8:120155591-120168541	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1804358	chr8:120155591-120179986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv612084	chr8:120156014-120165257	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv612085	chr8:120156014-120167195	Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv612086	chr8:120156014-120168541	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv612090	chr8:120156147-120165257	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv612101	chr8:120156923-120165257	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv612104	chr8:120157288-120165257	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv612107	chr8:120157583-120165257	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv612110	chr8:120158372-120165257	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13248274	NOV	cis	cerebellum	SCAN
rs13248274	SAMD12	cis	parietal	SCAN
rs13248274	MAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120156400-120165000	Weak transcription	Fetal Lung	lung
2	chr8:120158000-120165200	Weak transcription	NHEK	skin
3	chr8:120161400-120164400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr8:120162000-120163600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:120163200-120165600	Enhancers	Rectal Mucosa Donor 31	rectum

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