Variant report

Variant	rs248686
Chromosome Location	chr5:60354522-60354523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60351342..60352964-chr5:60353710..60356675,2	K562	blood:
2	chr5:60353410..60356120-chr5:60624338..60627119,3	MCF-7	breast:
3	chr5:60351609..60354587-chr5:60627368..60629896,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10071281	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153228	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs124899	0.86[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516321	1.00[ASN][1000 genomes]
rs12516552	1.00[ASN][1000 genomes]
rs12519764	1.00[ASN][1000 genomes]
rs12519810	1.00[ASN][1000 genomes]
rs12520484	1.00[ASN][1000 genomes]
rs12521434	1.00[ASN][1000 genomes]
rs1316649	1.00[ASN][1000 genomes]
rs13184350	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13187930	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158701	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158702	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159359	1.00[ASN][1000 genomes]
rs159361	1.00[ASN][1000 genomes]
rs159366	1.00[ASN][1000 genomes]
rs159368	1.00[ASN][1000 genomes]
rs159372	0.93[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17332419	1.00[ASN][1000 genomes]
rs181925	0.82[EUR][1000 genomes]
rs2059064	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080870	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248684	0.81[AFR][1000 genomes]
rs256373	1.00[ASN][1000 genomes]
rs28634357	1.00[ASN][1000 genomes]
rs295571	0.87[EUR][1000 genomes]
rs34089429	1.00[ASN][1000 genomes]
rs34099891	1.00[ASN][1000 genomes]
rs34155831	1.00[ASN][1000 genomes]
rs34279961	1.00[ASN][1000 genomes]
rs34596	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34622	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34628	1.00[ASN][1000 genomes]
rs34630	1.00[ASN][1000 genomes]
rs34632	1.00[ASN][1000 genomes]
rs34633	1.00[ASN][1000 genomes]
rs34642	0.93[CEU][hapmap]
rs34676209	1.00[ASN][1000 genomes]
rs34784445	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35078341	1.00[ASN][1000 genomes]
rs35957723	1.00[ASN][1000 genomes]
rs4647028	1.00[ASN][1000 genomes]
rs4647066	1.00[ASN][1000 genomes]
rs4647100	1.00[ASN][1000 genomes]
rs4647113	1.00[ASN][1000 genomes]
rs4647167	1.00[ASN][1000 genomes]
rs4647171	1.00[ASN][1000 genomes]
rs59521186	1.00[ASN][1000 genomes]
rs62365459	1.00[ASN][1000 genomes]
rs62367880	1.00[ASN][1000 genomes]
rs62367886	1.00[ASN][1000 genomes]
rs62367887	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370483	1.00[ASN][1000 genomes]
rs62372142	1.00[ASN][1000 genomes]
rs6893752	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71630091	1.00[ASN][1000 genomes]
rs7446842	1.00[ASN][1000 genomes]
rs7726671	1.00[ASN][1000 genomes]
rs9291706	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9763225	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs248686	ERCC8	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	chr5:60347400-60356000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:60349400-60370800	Weak transcription	HSMM	muscle
5	chr5:60350400-60362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:60350400-60371400	Weak transcription	NHDF-Ad	bronchial
7	chr5:60350600-60356000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:60350600-60378600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:60350800-60396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:60351200-60355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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