Variant report

Variant	rs4895902
Chromosome Location	chr6:131329259-131329260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1043598	0.92[JPT][hapmap]
rs10499174	0.92[JPT][hapmap]
rs12661081	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12664355	0.92[JPT][hapmap]
rs12965	0.92[JPT][hapmap]
rs13193246	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1332490	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1332491	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1338905	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17059681	0.92[JPT][hapmap]
rs17059683	0.92[JPT][hapmap]
rs17059698	0.92[JPT][hapmap]
rs17059702	0.92[JPT][hapmap]
rs17059896	0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs17059925	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17831009	0.92[JPT][hapmap]
rs1855077	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1888959	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1976982	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2007339	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2151069	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2225557	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2275063	0.92[JPT][hapmap]
rs3777450	0.92[JPT][hapmap]
rs3777453	0.92[JPT][hapmap]
rs3777463	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3822864	0.92[JPT][hapmap]
rs4897480	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897481	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897482	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897488	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4897490	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6569716	0.84[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6569718	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6569720	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569722	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6569725	0.86[EUR][1000 genomes]
rs6900810	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6908917	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6909134	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6928986	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6942081	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73623428	0.89[ASN][1000 genomes]
rs73774328	0.83[ASN][1000 genomes]
rs7742376	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7747881	0.92[JPT][hapmap]
rs7765007	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7765757	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7769153	0.85[JPT][hapmap]
rs9321268	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372988	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9689026	0.89[EUR][1000 genomes];0.83[ASN][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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4895902	AKAP7	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131322600-131333200	Weak transcription	Pancreas	Pancrea
2	chr6:131324000-131334200	Weak transcription	Small Intestine	intestine
3	chr6:131326000-131329400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:131326000-131333800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:131327000-131331200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:131327000-131333200	Weak transcription	Ovary	ovary
7	chr6:131327800-131329400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
8	chr6:131327800-131330600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
9	chr6:131327800-131331200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:131328000-131329800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:131328000-131329800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
12	chr6:131328000-131329800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:131328000-131329800	ZNF genes & repeats	Brain Substantia Nigra	brain
14	chr6:131328000-131329800	ZNF genes & repeats	Fetal Stomach	stomach
15	chr6:131328000-131330000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:131328000-131330200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr6:131328000-131330200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:131328000-131330200	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr6:131328200-131329800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:131328400-131329600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
21	chr6:131328400-131332200	Weak transcription	Brain Hippocampus Middle	brain
22	chr6:131328400-131334800	Weak transcription	A549	lung
23	chr6:131328800-131329400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
24	chr6:131328800-131330200	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr6:131329200-131329800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:131329200-131329800	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:131329200-131329800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:131329200-131330000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:131329200-131330200	ZNF genes & repeats	HepG2	liver
30	chr6:131329200-131330400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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