Variant report

Variant	rs16864042
Chromosome Location	chr1:171079005-171079006
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1080197	0.84[ASN][1000 genomes]
rs10911320	0.85[AFR][1000 genomes]
rs11812061	0.81[CHD][hapmap]
rs12059956	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12076145	0.82[AFR][1000 genomes]
rs12403297	0.84[ASN][1000 genomes]
rs12405599	0.81[ASN][1000 genomes]
rs12406572	0.81[ASN][1000 genomes]
rs17564980	0.81[ASN][1000 genomes]
rs17565336	0.81[CHD][hapmap]
rs17640463	0.80[CHD][hapmap]
rs2066529	0.84[ASN][1000 genomes]
rs2266780	0.81[ASN][1000 genomes]
rs2266782	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272797	0.81[CHD][hapmap]
rs2272800	0.81[CHD][hapmap]
rs28363536	0.84[ASN][1000 genomes]
rs28363537	0.84[ASN][1000 genomes]
rs28363541	0.84[ASN][1000 genomes]
rs28363571	0.81[ASN][1000 genomes]
rs7061710	0.81[ASN][1000 genomes]
rs72712649	0.84[ASN][1000 genomes]
rs7879505	0.87[GIH][hapmap]
rs7882773	0.87[GIH][hapmap]
rs7886938	0.81[CHD][hapmap]
rs7887142	0.81[CHD][hapmap]
rs7889839	0.81[CHD][hapmap]
rs909531	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16864042	KIFAP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171071000-171079600	Weak transcription	Left Ventricle	heart
2	chr1:171075600-171079800	Weak transcription	Pancreas	Pancrea
3	chr1:171076800-171079600	Enhancers	Fetal Lung	lung
4	chr1:171077600-171081800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:171077800-171080000	Weak transcription	Small Intestine	intestine
6	chr1:171078000-171079600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:171078200-171079400	Strong transcription	Liver	Liver
8	chr1:171078200-171079400	Weak transcription	Right Atrium	heart
9	chr1:171078200-171079600	Weak transcription	Aorta	Aorta
10	chr1:171078400-171079400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:171078400-171079800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:171078600-171079800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:171079000-171081000	Enhancers	NHLF	lung

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