Variant report

Variant	rs124899
Chromosome Location	chr5:60468683-60468684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
2	chr5:60454738..60463245-chr5:60465333..60477980,25	K562	blood:
3	chr5:60464487..60466680-chr5:60468300..60471010,2	K562	blood:
4	chr5:60457581..60462290-chr5:60466231..60469667,6	K562	blood:

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10071281	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153228	1.00[ASN][1000 genomes]
rs12516321	0.85[GIH][hapmap];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	1.00[ASN][1000 genomes]
rs13187930	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158701	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs158702	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	0.85[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059064	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080870	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161198	0.86[AFR][1000 genomes]
rs248686	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]
rs256373	1.00[ASN][1000 genomes]
rs28634357	1.00[ASN][1000 genomes]
rs295571	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34089429	1.00[ASN][1000 genomes]
rs34155831	1.00[ASN][1000 genomes]
rs34279961	1.00[ASN][1000 genomes]
rs34596	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34622	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[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	0.85[CEU][hapmap]
rs34676209	1.00[ASN][1000 genomes]
rs34784445	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]
rs62365459	1.00[ASN][1000 genomes]
rs62367880	1.00[ASN][1000 genomes]
rs62367886	1.00[ASN][1000 genomes]
rs62367887	1.00[ASN][1000 genomes]
rs62370483	1.00[ASN][1000 genomes]
rs62372142	1.00[ASN][1000 genomes]
rs6893752	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71630091	1.00[ASN][1000 genomes]
rs7446842	1.00[ASN][1000 genomes]
rs9291706	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9763225	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs124899	mimitin	cis	multi-tissue	Pritchard
rs124899	ERCC8	cis	multi-tissue	Pritchard
rs124899	ERCC8	cis	parietal	SCAN
rs124899	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60460000-60469000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:60460000-60473000	Weak transcription	HSMM	muscle
3	chr5:60460400-60470400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:60460400-60475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:60463800-60472600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:60466800-60473000	Weak transcription	Fetal Stomach	stomach
7	chr5:60468600-60484400	Weak transcription	Aorta	Aorta

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