Variant report

Variant	rs11951504
Chromosome Location	chr5:60372438-60372439
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10471503	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11951606	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357828	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158563	0.85[ASN][1000 genomes]
rs158565	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158566	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158567	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158568	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158569	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158916	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.85[ASN][1000 genomes]
rs158920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs158925	0.85[ASN][1000 genomes]
rs158926	0.85[ASN][1000 genomes]
rs158928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1609041	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.85[ASN][1000 genomes]
rs162229	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162231	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162232	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162233	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162235	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs162236	0.85[ASN][1000 genomes]
rs162237	0.84[ASN][1000 genomes]
rs162239	0.85[ASN][1000 genomes]
rs162240	0.85[ASN][1000 genomes]
rs162250	0.85[ASN][1000 genomes]
rs167912	0.85[ASN][1000 genomes]
rs170658	0.81[ASN][1000 genomes]
rs182351	0.85[ASN][1000 genomes]
rs2306350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs2306351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs248678	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs248679	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs248680	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2619891	0.85[ASN][1000 genomes]
rs2619892	0.85[ASN][1000 genomes]
rs290504	0.85[ASN][1000 genomes]
rs290505	0.85[ASN][1000 genomes]
rs2909851	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2928243	0.85[ASN][1000 genomes]
rs2928246	0.85[ASN][1000 genomes]
rs2950232	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs295556	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295557	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295565	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs295567	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs329614	0.85[ASN][1000 genomes]
rs329619	0.85[ASN][1000 genomes]
rs329620	0.85[ASN][1000 genomes]
rs329627	0.85[ASN][1000 genomes]
rs34425764	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34595	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34598	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34599	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34640	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34641	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap]
rs4647108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6449509	1.00[CEU][hapmap]
rs6449510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6871236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445953	0.90[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs9291704	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11951504	ERCC8	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 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	chr5:60350600-60378600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:60350800-60396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:60362800-60377200	Weak transcription	Psoas Muscle	Psoas
6	chr5:60365600-60376400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:60365600-60387000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:60366400-60397400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:60367200-60382200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:60367400-60379400	Weak transcription	HMEC	breast
11	chr5:60367400-60385200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:60367400-60386800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:60367400-60399400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:60367600-60372600	Weak transcription	NHEK	skin
15	chr5:60367600-60378400	Weak transcription	Primary T cells from cord blood	blood
16	chr5:60367600-60380000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:60367600-60380000	Weak transcription	Liver	Liver
18	chr5:60367600-60398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:60367800-60403800	Weak transcription	Primary B cells from cord blood	blood
20	chr5:60368000-60372600	Weak transcription	A549	lung
21	chr5:60368200-60374800	Weak transcription	Fetal Intestine Large	intestine
22	chr5:60368200-60377600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:60368200-60390600	Weak transcription	Fetal Intestine Small	intestine
24	chr5:60368200-60397600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:60368200-60402000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:60368400-60390200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:60368600-60378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:60368600-60381200	Weak transcription	K562	blood
29	chr5:60369000-60400200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr5:60369400-60388200	Weak transcription	Gastric	stomach
31	chr5:60369600-60378800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:60369800-60396400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:60370000-60372800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:60370000-60377600	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:60370200-60395600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:60371200-60372600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:60371400-60372600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:60371400-60382800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr5:60371600-60398000	Weak transcription	HSMM	muscle
40	chr5:60371800-60387400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:60372200-60373600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:60372400-60373400	Enhancers	Primary hematopoietic stem cells	blood
43	chr5:60372400-60373600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:60372400-60379200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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