Variant report

Variant	rs185354
Chromosome Location	chr5:60460617-60460618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:60460397-60460803	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:60456297..60461829-chr5:60626718..60632720,8	K562	blood:
2	chr5:60428916..60430499-chr5:60459028..60461996,2	K562	blood:
3	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
4	chr5:60459450..60460955-chr5:60472059..60474565,2	MCF-7	breast:
5	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:

Variant related genes	Relation type
SMIM15	TF binding region
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10471502	0.84[AFR][1000 genomes]
rs10939882	0.82[EUR][1000 genomes]
rs11951076	0.81[EUR][1000 genomes]
rs11957772	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs124898	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12518865	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13168191	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13171576	0.82[EUR][1000 genomes]
rs1382914	0.84[EUR][1000 genomes]
rs158564	0.87[EUR][1000 genomes]
rs158571	0.82[EUR][1000 genomes]
rs158915	0.83[EUR][1000 genomes]
rs158919	0.83[EUR][1000 genomes]
rs158923	0.84[EUR][1000 genomes]
rs158924	0.84[EUR][1000 genomes]
rs158931	0.83[EUR][1000 genomes]
rs158932	0.82[EUR][1000 genomes]
rs158933	0.82[EUR][1000 genomes]
rs158934	0.82[EUR][1000 genomes]
rs158935	0.82[EUR][1000 genomes]
rs158936	0.82[EUR][1000 genomes]
rs159357	0.93[AFR][1000 genomes]
rs159358	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159371	0.93[AFR][1000 genomes]
rs159374	0.91[AFR][1000 genomes]
rs159375	0.91[AFR][1000 genomes]
rs159376	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs159377	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159378	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159380	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs159537	0.81[EUR][1000 genomes]
rs162234	0.87[EUR][1000 genomes]
rs162238	0.86[EUR][1000 genomes]
rs162241	0.85[EUR][1000 genomes]
rs162242	0.87[EUR][1000 genomes]
rs162244	0.86[EUR][1000 genomes]
rs162247	0.85[EUR][1000 genomes]
rs162248	0.84[EUR][1000 genomes]
rs172348	0.84[EUR][1000 genomes]
rs172945	0.86[EUR][1000 genomes]
rs182410	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs187459	0.93[EUR][1000 genomes]
rs2080869	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2112365	0.82[EUR][1000 genomes]
rs2263514	0.84[EUR][1000 genomes]
rs248677	0.91[EUR][1000 genomes]
rs248682	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs248683	0.81[AFR][1000 genomes]
rs248685	0.94[EUR][1000 genomes]
rs2545475	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2545478	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2545503	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs256375	0.93[AFR][1000 genomes]
rs256376	0.89[AFR][1000 genomes]
rs2650512	0.84[EUR][1000 genomes]
rs2650517	0.84[EUR][1000 genomes]
rs2694530	0.84[EUR][1000 genomes]
rs2694531	0.84[EUR][1000 genomes]
rs290503	0.86[EUR][1000 genomes]
rs290506	0.86[EUR][1000 genomes]
rs290507	0.86[EUR][1000 genomes]
rs290516	0.82[EUR][1000 genomes]
rs2950235	0.84[EUR][1000 genomes]
rs295522	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs295524	0.93[AFR][1000 genomes]
rs295531	0.82[AFR][1000 genomes]
rs295532	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs295533	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs295551	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs295560	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs295561	0.88[AFR][1000 genomes]
rs295563	0.88[AFR][1000 genomes]
rs295564	0.88[AFR][1000 genomes]
rs295566	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs295569	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs295573	0.91[AFR][1000 genomes]
rs295578	0.88[AFR][1000 genomes]
rs295579	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs295582	0.84[EUR][1000 genomes]
rs298629	0.81[EUR][1000 genomes]
rs3108388	0.85[EUR][1000 genomes]
rs329622	0.86[EUR][1000 genomes]
rs329623	0.86[EUR][1000 genomes]
rs329625	0.86[EUR][1000 genomes]
rs329626	0.84[EUR][1000 genomes]
rs34593	0.90[EUR][1000 genomes]
rs34609	0.81[EUR][1000 genomes]
rs34610	0.91[AFR][1000 genomes]
rs34613	0.81[EUR][1000 genomes]
rs34614	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34616	0.81[EUR][1000 genomes]
rs34617	0.81[EUR][1000 genomes]
rs34621	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34623	0.94[AFR][1000 genomes]
rs34624	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34625	0.82[EUR][1000 genomes]
rs34636	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34637	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34639	0.93[EUR][1000 genomes]
rs34644	0.93[EUR][1000 genomes]
rs39661	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs40084	0.93[EUR][1000 genomes]
rs40421	0.81[AFR][1000 genomes]
rs4141502	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4699969	0.82[EUR][1000 genomes]
rs56409036	0.85[EUR][1000 genomes]
rs6868884	0.84[AFR][1000 genomes]
rs6869073	0.88[AFR][1000 genomes]
rs6878124	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6886481	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs723276	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7701839	0.91[EUR][1000 genomes]
rs7706753	0.80[EUR][1000 genomes]
rs810883	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs810884	0.93[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs185354	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60459400-60463400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:60459400-60463400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:60459600-60463400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:60459600-60463400	Weak transcription	HUVEC	blood vessel
5	chr5:60459600-60464600	Weak transcription	Stomach Mucosa	stomach
6	chr5:60459800-60461000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:60459800-60461200	Enhancers	Ovary	ovary
8	chr5:60459800-60463400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:60459800-60463400	Weak transcription	Osteobl	bone
10	chr5:60460000-60461000	Weak transcription	Brain Germinal Matrix	brain
11	chr5:60460000-60461600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:60460000-60469000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr5:60460000-60473000	Weak transcription	HSMM	muscle
14	chr5:60460200-60460800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:60460200-60461000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:60460200-60461200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:60460200-60461200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:60460200-60461200	Weak transcription	Fetal Brain Female	brain
19	chr5:60460200-60461200	Weak transcription	A549	lung
20	chr5:60460200-60463400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:60460200-60463400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:60460400-60460800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:60460400-60461000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:60460400-60461000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:60460400-60461000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:60460400-60461200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:60460400-60461200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:60460400-60461200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:60460400-60461200	Enhancers	Fetal Brain Male	brain
30	chr5:60460400-60461200	Weak transcription	Left Ventricle	heart
31	chr5:60460400-60462000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:60460400-60464400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:60460400-60467200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:60460400-60470400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:60460400-60475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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