Variant report

Variant	rs6425468
Chromosome Location	chr1:171854198-171854199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015008	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1022541	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1040517	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737337	0.86[ASN][1000 genomes]
rs10737338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753203	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753205	0.85[ASN][1000 genomes]
rs1076700	0.85[ASN][1000 genomes]
rs10798695	0.85[ASN][1000 genomes]
rs10798701	0.85[ASN][1000 genomes]
rs10798702	0.85[ASN][1000 genomes]
rs10798705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798706	0.84[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs10798716	0.85[ASN][1000 genomes]
rs10798722	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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1118173	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs12021814	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12024869	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs12025243	0.91[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs12029015	0.84[EUR][1000 genomes]
rs12040254	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12047542	0.85[EUR][1000 genomes]
rs12239702	0.81[ASN][1000 genomes]
rs12405583	0.85[ASN][1000 genomes]
rs12747663	0.85[EUR][1000 genomes]
rs1535301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1555100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1972340	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980488	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145383	0.91[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs2206543	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2235696	0.85[ASN][1000 genomes]
rs2421915	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs2421947	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2901600	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs34906981	0.92[EUR][1000 genomes]
rs4500358	0.85[ASN][1000 genomes]
rs4596936	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4916235	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916400	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916401	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];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916402	0.85[ASN][1000 genomes]
rs4916403	0.85[ASN][1000 genomes]
rs4916404	0.87[ASW][hapmap];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[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916411	0.92[EUR][1000 genomes]
rs6425454	0.85[ASN][1000 genomes]
rs6425455	0.85[ASN][1000 genomes]
rs6425456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425484	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6425518	0.84[EUR][1000 genomes]
rs6657315	0.85[ASN][1000 genomes]
rs6660011	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683945	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6685974	0.85[ASN][1000 genomes]
rs6686260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6689231	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs6690848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6701033	0.89[CHD][hapmap]
rs6702944	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs71523161	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs742509	0.85[ASN][1000 genomes]
rs742510	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs7514627	0.85[ASN][1000 genomes]
rs7517331	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526653	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7554700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7554935	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926545	0.84[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs926546	0.84[ASN][1000 genomes]
rs965051	0.84[CHB][hapmap];0.85[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	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv831893	chr1:171802450-171985000	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6425468	KIFAP3	cis	parietal	SCAN
rs6425468	NME7	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171844400-171858200	Weak transcription	Left Ventricle	heart
2	chr1:171852800-171854200	Enhancers	GM12878-XiMat	blood
3	chr1:171853000-171854200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:171853000-171854200	Enhancers	Brain Substantia Nigra	brain
5	chr1:171853000-171854200	Enhancers	Dnd41	blood
6	chr1:171853000-171854400	Enhancers	Brain Cingulate Gyrus	brain
7	chr1:171853000-171854400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:171853000-171855200	Enhancers	Brain Hippocampus Middle	brain
9	chr1:171853200-171854400	Enhancers	Brain Angular Gyrus	brain
10	chr1:171853400-171854200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:171853400-171854400	Enhancers	HMEC	breast
12	chr1:171853600-171854200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:171853600-171854400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:171853600-171854400	Enhancers	NHEK	skin
15	chr1:171854000-171866000	Weak transcription	Brain Anterior Caudate	brain

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