Variant report

Variant	rs1346787
Chromosome Location	chr2:56092612-56092613
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	chr2:56089463..56091242-chr2:56092326..56094493,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11125607	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125608	0.93[ASN][1000 genomes]
rs12478566	0.83[ASN][1000 genomes]
rs1344732	0.81[ASN][1000 genomes]
rs1346781	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1346783	0.86[ASN][1000 genomes]
rs1346790	0.96[ASN][1000 genomes]
rs1367225	0.81[ASN][1000 genomes]
rs1367226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367228	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1430189	0.84[ASN][1000 genomes]
rs1430190	0.81[ASN][1000 genomes]
rs1430191	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1430203	0.93[ASN][1000 genomes]
rs1897114	0.93[ASN][1000 genomes]
rs1960050	0.91[ASN][1000 genomes]
rs1985160	0.81[ASN][1000 genomes]
rs1985162	0.81[ASN][1000 genomes]
rs2052933	0.84[ASN][1000 genomes]
rs2115876	0.89[ASN][1000 genomes]
rs2115878	0.86[ASN][1000 genomes]
rs3791676	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4352264	0.98[ASN][1000 genomes]
rs4672074	0.86[ASN][1000 genomes]
rs6545523	0.83[ASN][1000 genomes]
rs6545526	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545527	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708796	0.89[ASN][1000 genomes]
rs6712017	0.84[ASN][1000 genomes]
rs6714513	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6733730	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6743114	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749785	0.82[ASN][1000 genomes]
rs6751403	0.91[ASN][1000 genomes]
rs6753814	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6757057	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7426380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7572523	0.89[ASN][1000 genomes]
rs7607070	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7609520	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs934278	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1346787	CCDC85A	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56089200-56095000	Weak transcription	Aorta	Aorta
2	chr2:56089200-56097000	Weak transcription	Lung	lung
3	chr2:56089200-56112200	Weak transcription	Pancreas	Pancrea
4	chr2:56089400-56093800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:56089400-56097000	Weak transcription	Right Atrium	heart
6	chr2:56089600-56097000	Weak transcription	HSMMtube	muscle
7	chr2:56089800-56098000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:56090000-56107600	Weak transcription	Fetal Stomach	stomach
9	chr2:56090200-56107400	Weak transcription	Fetal Lung	lung
10	chr2:56090400-56094800	Weak transcription	Adipose Nuclei	Adipose
11	chr2:56090800-56092800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:56090800-56094200	Weak transcription	NHEK	skin
13	chr2:56090800-56094800	Weak transcription	Placenta	Placenta
14	chr2:56090800-56095000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:56091000-56093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:56091200-56102600	Weak transcription	Hela-S3	cervix
17	chr2:56091800-56092800	Enhancers	Ovary	ovary
18	chr2:56091800-56093000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:56091800-56093000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:56092000-56093400	Enhancers	A549	lung
21	chr2:56092000-56093600	Enhancers	NHDF-Ad	bronchial
22	chr2:56092000-56099200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:56092200-56094000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:56092400-56093000	Enhancers	NH-A	brain
25	chr2:56092400-56093000	Enhancers	NHLF	lung
26	chr2:56092400-56093600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:56092400-56094800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:56092400-56100000	Genic enhancers	Osteobl	bone
29	chr2:56092400-56111600	Genic enhancers	HUVEC	blood vessel
30	chr2:56092600-56092800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:56092600-56092800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:56092600-56092800	Enhancers	Brain Anterior Caudate	brain
33	chr2:56092600-56092800	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:56092600-56093000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:56092600-56093000	Enhancers	HMEC	breast
36	chr2:56092600-56102600	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links