Variant report

Variant	rs839136
Chromosome Location	chr12:86528635-86528636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1024076	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs1689361	0.94[ASW][hapmap];0.96[CEU][hapmap];0.92[GIH][hapmap];0.96[LWK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs1689363	0.94[ASW][hapmap];0.96[CEU][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1698756	0.96[CEU][hapmap];0.95[TSI][hapmap]
rs1698787	0.85[CHB][hapmap]
rs17013647	0.80[CHD][hapmap]
rs2934143	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839092	0.96[CEU][hapmap];0.80[YRI][hapmap]
rs839093	0.94[ASW][hapmap];0.96[CEU][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs839095	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs839096	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs839097	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs839133	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839137	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs839145	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839146	0.96[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs839173	0.89[CEU][hapmap];0.97[TSI][hapmap]
rs839174	0.89[ASW][hapmap];0.96[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs839175	0.84[JPT][hapmap];0.83[YRI][hapmap]
rs839176	0.84[YRI][hapmap]
rs839177	0.96[CEU][hapmap]
rs839179	0.94[ASW][hapmap];0.96[CEU][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap]
rs839180	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844431	0.95[CEU][hapmap];0.84[JPT][hapmap]
rs863394	0.87[CHB][hapmap]
rs863940	0.89[ASW][hapmap];0.92[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv470311	chr12:86484366-86550783	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3442004	chr12:86514695-86599965	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2753278	chr12:86522507-86555154	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs839136	CEP290	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86526200-86531200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:86526800-86529800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr12:86527000-86528800	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr12:86527400-86529800	Weak transcription	Fetal Heart	heart
5	chr12:86528000-86528800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:86528000-86529400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:86528000-86529400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr12:86528000-86529400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:86528200-86528800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:86528200-86528800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:86528200-86528800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:86528200-86529000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:86528200-86529000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:86528200-86530400	Enhancers	Brain Germinal Matrix	brain
15	chr12:86528200-86531000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:86528400-86528800	Enhancers	A549	lung
17	chr12:86528400-86529000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr12:86528600-86528800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:86528600-86529000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:86528600-86529600	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links