Variant report

Variant	rs1526896
Chromosome Location	chr5:60359710-60359711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10805374	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10939879	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10939881	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10939882	0.87[AFR][1000 genomes]
rs11739952	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11951076	0.83[AFR][1000 genomes]
rs12516995	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12517310	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12518404	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12518792	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12652830	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12652878	0.80[EUR][1000 genomes]
rs12653132	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655209	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12655603	0.81[ASN][1000 genomes]
rs1382917	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1460961	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1471488	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1479645	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs159535	0.93[EUR][1000 genomes]
rs159536	0.92[EUR][1000 genomes]
rs159537	0.82[AFR][1000 genomes]
rs17332824	0.80[EUR][1000 genomes]
rs17392014	0.80[EUR][1000 genomes]
rs17419290	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17444495	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983484	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049579	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28436304	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2898309	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34608	0.93[EUR][1000 genomes]
rs34619	0.91[EUR][1000 genomes]
rs3797559	0.83[ASN][1000 genomes]
rs4642318	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4647052	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647137	0.81[EUR][1000 genomes]
rs4647150	0.80[EUR][1000 genomes]
rs4699969	0.87[AFR][1000 genomes]
rs4700402	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4700404	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4700407	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55738840	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55814394	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56025209	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56031340	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56284222	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56350217	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58646987	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60858663	0.81[ASN][1000 genomes]
rs61017995	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62365455	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62365458	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367862	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367872	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62367878	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62367879	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367885	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62367903	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62372133	0.81[ASN][1000 genomes]
rs62372134	0.81[ASN][1000 genomes]
rs6449512	0.87[EUR][1000 genomes]
rs67490467	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68104763	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726824	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72757187	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72759206	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72759215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701398	0.80[EUR][1000 genomes]
rs7706753	0.85[AFR][1000 genomes]
rs7709522	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7713481	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7714396	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7722373	0.90[ASN][1000 genomes]
rs7723349	0.92[ASN][1000 genomes]
rs7723901	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7734205	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7737276	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs868791	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888799	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs976630	0.83[ASN][1000 genomes]
rs976631	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1526896	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs1526896	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
2	chr5:60347200-60379200	Weak transcription	Ovary	ovary
3	chr5:60349400-60370800	Weak transcription	HSMM	muscle
4	chr5:60350400-60362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:60350400-60371400	Weak transcription	NHDF-Ad	bronchial
6	chr5:60350600-60378600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:60350800-60396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:60354800-60361400	Weak transcription	Pancreas	Pancrea
9	chr5:60356200-60360000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:60357800-60369000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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