Variant report

Variant	rs6433687
Chromosome Location	chr2:178534324-178534325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178533626..178535228-chr2:178535564..178538374,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10497493	0.82[YRI][hapmap]
rs10497497	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11679730	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680632	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs12618150	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620285	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000926	0.93[YRI][hapmap]
rs13017234	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017429	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025391	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025904	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026012	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028757	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317945	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358327	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405716	0.93[ASW][hapmap];0.92[YRI][hapmap]
rs1446839	0.80[EUR][1000 genomes]
rs1527399	0.93[YRI][hapmap]
rs1527400	0.93[ASW][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap]
rs1527402	0.92[YRI][hapmap]
rs1527403	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527410	0.91[YRI][hapmap]
rs1534305	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1544001	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544003	0.91[YRI][hapmap]
rs1547580	0.88[YRI][hapmap]
rs1547581	0.93[YRI][hapmap]
rs1918345	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918346	0.93[EUR][1000 genomes]
rs1918347	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1997206	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997207	0.80[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997208	0.93[YRI][hapmap]
rs2091442	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222712	0.80[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365620	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886422	0.92[YRI][hapmap]
rs4110134	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341975	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893970	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893973	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893975	0.85[ASW][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap]
rs4893976	0.93[YRI][hapmap]
rs4893978	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893979	0.95[EUR][1000 genomes]
rs5025340	0.80[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433685	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433686	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433688	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721360	0.90[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723031	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6723063	0.86[ASN][1000 genomes]
rs6746233	0.83[EUR][1000 genomes]
rs6755382	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6756918	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7422544	0.92[YRI][hapmap]
rs7560080	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560514	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573345	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7577552	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578901	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586934	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593744	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593753	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7597640	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941271	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6433687	TTC30B	cis	parietal	SCAN
rs6433687	PRKRA	cis	parietal	SCAN
rs6433687	AGPS	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178531400-178534800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:178531400-178535800	Weak transcription	GM12878-XiMat	blood
3	chr2:178531400-178540000	Weak transcription	K562	blood
4	chr2:178531800-178535000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:178532800-178534800	Weak transcription	Psoas Muscle	Psoas
6	chr2:178532800-178537000	Enhancers	Fetal Kidney	kidney
7	chr2:178532800-178538000	Weak transcription	HSMM	muscle
8	chr2:178533400-178535800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:178533800-178536600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
10	chr2:178533800-178536600	Enhancers	Dnd41	blood
11	chr2:178534000-178537200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:178534200-178534800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr2:178534200-178535400	Enhancers	Liver	Liver
14	chr2:178534200-178537000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links