Variant report

Variant	rs12902047
Chromosome Location	chr15:41915522-41915523
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11630972	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs11631051	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11634582	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11634804	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11636523	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap]
rs1197671	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1197672	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1197705	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs12906666	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12914573	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917387	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs17676332	1.00[JPT][hapmap]
rs17677098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap]
rs17677757	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.95[MKK][hapmap]
rs17678310	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17733703	0.88[EUR][1000 genomes]
rs2178003	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs2925339	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap]
rs34040639	1.00[JPT][hapmap]
rs34802546	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35698486	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57359439	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60526934	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62003878	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66593163	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs7183061	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042809	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs9646193	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902047	SPTBN5	cis	lung	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41913800-41939400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:41914200-41924600	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:41914200-41935800	Weak transcription	Gastric	stomach
4	chr15:41914400-41917200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:41914400-41925800	Weak transcription	Lung	lung
6	chr15:41914600-41917600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr15:41914600-41918000	Weak transcription	Spleen	Spleen
8	chr15:41914600-41922800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:41914600-41924400	Weak transcription	Ovary	ovary
10	chr15:41914600-41924600	Weak transcription	Left Ventricle	heart
11	chr15:41914800-41916000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:41915000-41915600	Enhancers	Dnd41	blood
13	chr15:41915000-41921600	Weak transcription	Psoas Muscle	Psoas
14	chr15:41915000-41921600	Weak transcription	NHDF-Ad	bronchial
15	chr15:41915000-41922000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:41915000-41924200	Weak transcription	Brain Anterior Caudate	brain
17	chr15:41915000-41924600	Weak transcription	Right Atrium	heart
18	chr15:41915000-41926000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:41915000-41927400	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:41915200-41922200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:41915200-41924400	Weak transcription	Brain Substantia Nigra	brain
22	chr15:41915400-41917200	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links