Variant report

Variant	rs1429556
Chromosome Location	chr15:49707670-49707671
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10467992	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs10519230	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs10851475	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs10851476	0.84[JPT][hapmap]
rs11070687	0.85[JPT][hapmap]
rs11070692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070693	0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs11631040	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs11631687	0.81[AFR][1000 genomes]
rs11636795	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs11638378	0.86[AFR][1000 genomes]
rs11852524	0.91[YRI][hapmap]
rs11854667	0.84[JPT][hapmap]
rs11858114	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs12439429	0.91[CHB][hapmap]
rs12439479	0.87[AFR][1000 genomes]
rs12909779	0.85[JPT][hapmap]
rs12913745	0.87[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs12916840	0.85[JPT][hapmap]
rs16962440	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs16962486	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16962490	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs1816293	0.84[JPT][hapmap]
rs1904316	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2086256	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs2127241	0.92[CEU][hapmap]
rs2127242	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs2163095	0.85[JPT][hapmap]
rs2163096	0.84[JPT][hapmap]
rs2219812	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs2580926	0.92[CEU][hapmap]
rs2663088	0.92[CEU][hapmap]
rs2899430	0.92[CEU][hapmap]
rs3098620	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs4316697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4421927	0.85[JPT][hapmap]
rs6493361	0.88[CEU][hapmap]
rs6493363	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7162360	0.84[JPT][hapmap]
rs735495	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs754165	0.92[CEU][hapmap]
rs754166	0.92[CEU][hapmap]
rs8024102	0.84[JPT][hapmap]
rs8025952	0.92[CEU][hapmap]
rs8031892	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034747	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040075	0.92[CEU][hapmap]
rs919447	0.84[JPT][hapmap]
rs981612	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1429556	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49703000-49709600	Weak transcription	Fetal Lung	lung
2	chr15:49707200-49708600	Enhancers	NHDF-Ad	bronchial
3	chr15:49707200-49708600	Enhancers	Osteobl	bone
4	chr15:49707200-49709000	Enhancers	Hela-S3	cervix
5	chr15:49707400-49707800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr15:49707400-49707800	Enhancers	NH-A	brain
7	chr15:49707400-49708200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:49707400-49708400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:49707400-49708400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:49707400-49708400	Enhancers	HUVEC	blood vessel
11	chr15:49707400-49708600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:49707400-49708600	Enhancers	HMEC	breast
13	chr15:49707400-49708800	Enhancers	NHLF	lung
14	chr15:49707600-49708400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:49707600-49708400	Enhancers	NHEK	skin
16	chr15:49707600-49709400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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