Variant report

Variant	rs35556055
Chromosome Location	chr15:75253414-75253415
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	chr15:75252668..75254763-chr15:75257442..75260198,2	K562	blood:
2	chr15:75250701..75253480-chr15:75254260..75256998,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11072512	0.83[MEX][hapmap]
rs11072513	0.81[CEU][hapmap]
rs11072514	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs1127796	0.83[MEX][hapmap]
rs1133322	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs1133323	0.81[CEU][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs11630087	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630592	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11630918	0.91[MEX][hapmap]
rs11633472	0.91[MEX][hapmap]
rs11636892	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638130	0.91[MEX][hapmap]
rs11639413	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11854704	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs11856413	0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs12901190	0.81[CEU][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs12903370	0.82[AMR][1000 genomes]
rs12904326	0.80[AMR][1000 genomes]
rs12909335	0.81[CEU][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs12912343	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912839	0.80[AMR][1000 genomes]
rs2044157	0.84[AMR][1000 genomes]
rs2415251	0.85[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34063670	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34307821	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34799293	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35882241	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812945	0.92[MEX][hapmap];0.85[TSI][hapmap]
rs4886413	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886417	0.84[MEX][hapmap]
rs4886648	0.84[MEX][hapmap]
rs56338926	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62029217	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495664	0.80[AMR][1000 genomes]

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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1612	chr15:75247725-75281284	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs35556055	SCAMP2	cis	Whole Blood	GTEx
rs35556055	MAN2C1	cis	parietal	SCAN
rs35556055	ULK3	cis	parietal	SCAN
rs35556055	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs35556055	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs35556055	TLE3	cis	cerebellum	SCAN
rs35556055	SKIL	trans	cerebellum	SCAN
rs35556055	SCAMP5	cis	Artery Tibial	GTEx
rs35556055	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs35556055	SCAMP2	cis	parietal	SCAN
rs35556055	MPI	cis	lymphoblastoid	seeQTL
rs35556055	SCAMP5	cis	lung	GTEx
rs35556055	CYP1A1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75251800-75253600	Enhancers	HUVEC	blood vessel
2	chr15:75252000-75255400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:75252000-75256400	Weak transcription	Lung	lung
4	chr15:75252000-75257200	Weak transcription	Pancreas	Pancrea
5	chr15:75252400-75255600	Enhancers	Brain Germinal Matrix	brain
6	chr15:75252400-75256800	Weak transcription	NHDF-Ad	bronchial
7	chr15:75252600-75254000	Enhancers	Fetal Lung	lung
8	chr15:75252600-75254200	Enhancers	Hela-S3	cervix
9	chr15:75252800-75255800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:75253000-75253800	Weak transcription	Placenta	Placenta
11	chr15:75253000-75254000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:75253000-75254200	Enhancers	Stomach Mucosa	stomach
13	chr15:75253000-75255800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:75253200-75254200	Enhancers	A549	lung
15	chr15:75253400-75253600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:75253400-75253800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
17	chr15:75253400-75254000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:75253400-75254000	Enhancers	Rectal Mucosa Donor 31	rectum

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