Variant report

Variant	rs6657936
Chromosome Location	chr1:58528820-58528821
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10443219	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10443242	0.82[CHB][hapmap];0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs10443244	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10443245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10443246	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10443247	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889081	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10889082	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207162	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11207163	0.83[AFR][1000 genomes]
rs11207165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11207166	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs12124142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12563473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1408925	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17116775	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17116802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025616	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2025618	1.00[YRI][hapmap]
rs2806403	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2808814	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs2808822	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs34678610	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3753508	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753509	1.00[ASN][1000 genomes]
rs57920068	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58537714	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587800	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6657553	0.99[EUR][1000 genomes]
rs6677854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7515158	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7516066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7527900	0.94[EUR][1000 genomes]
rs7527995	1.00[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7548316	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527673	chr1:58526235-58531627	Weak transcription Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6657936	PRAMEF22	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58525800-58529800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:58525800-58531600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:58526000-58530000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:58526400-58529800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:58526600-58530000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:58526600-58531200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:58526800-58531400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:58527400-58530200	Weak transcription	Fetal Brain Female	brain
9	chr1:58528000-58529200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:58528000-58529400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:58528000-58529400	Enhancers	HMEC	breast
12	chr1:58528000-58529400	Enhancers	NHEK	skin
13	chr1:58528000-58529600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:58528200-58529200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:58528400-58529000	Weak transcription	Fetal Brain Male	brain
16	chr1:58528600-58529000	Enhancers	Hela-S3	cervix

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