Variant report

Variant	rs162247
Chromosome Location	chr5:60290199-60290200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10076937	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10939882	0.81[EUR][1000 genomes]
rs11951076	0.80[EUR][1000 genomes]
rs11957772	0.89[EUR][1000 genomes]
rs124898	0.88[EUR][1000 genomes]
rs12518865	0.89[EUR][1000 genomes]
rs13155076	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13168191	0.89[EUR][1000 genomes]
rs13171576	0.81[EUR][1000 genomes]
rs13359074	0.86[EUR][1000 genomes]
rs1382914	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs158564	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs158570	0.89[EUR][1000 genomes]
rs158571	0.94[EUR][1000 genomes]
rs158915	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs158919	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs158921	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs158923	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs158924	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs158927	0.85[AFR][1000 genomes]
rs158929	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs158931	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs158932	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs158933	0.94[EUR][1000 genomes]
rs158934	0.94[EUR][1000 genomes]
rs158935	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs158936	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs158938	0.85[AFR][1000 genomes]
rs159358	0.88[EUR][1000 genomes]
rs159376	0.86[EUR][1000 genomes]
rs159377	0.88[EUR][1000 genomes]
rs159378	0.88[EUR][1000 genomes]
rs159380	0.88[EUR][1000 genomes]
rs159537	0.80[EUR][1000 genomes]
rs162228	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs162234	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs162238	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs162241	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs162242	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs162244	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs162248	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs162251	0.80[EUR][1000 genomes]
rs169700	0.89[AFR][1000 genomes]
rs172348	0.96[EUR][1000 genomes]
rs172945	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs182410	0.88[EUR][1000 genomes]
rs185354	0.85[EUR][1000 genomes]
rs187459	0.91[EUR][1000 genomes]
rs2080869	0.89[EUR][1000 genomes]
rs2112365	0.81[EUR][1000 genomes]
rs2120955	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2263514	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs248677	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs248682	0.89[EUR][1000 genomes]
rs248685	0.89[EUR][1000 genomes]
rs2545475	0.89[EUR][1000 genomes]
rs2545478	0.89[EUR][1000 genomes]
rs2545503	0.89[EUR][1000 genomes]
rs2650506	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2650512	0.96[EUR][1000 genomes]
rs2650517	0.96[EUR][1000 genomes]
rs2694518	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2694530	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2694531	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28407266	0.89[EUR][1000 genomes]
rs290503	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs290506	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs290507	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs290509	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs290514	0.85[AFR][1000 genomes]
rs290515	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs290516	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2950235	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295522	0.88[EUR][1000 genomes]
rs295532	0.87[EUR][1000 genomes]
rs295533	0.89[EUR][1000 genomes]
rs295551	0.89[EUR][1000 genomes]
rs295560	0.89[EUR][1000 genomes]
rs295566	0.89[EUR][1000 genomes]
rs295569	0.88[EUR][1000 genomes]
rs295579	0.85[EUR][1000 genomes]
rs298629	0.81[EUR][1000 genomes]
rs3108388	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3117	0.87[EUR][1000 genomes]
rs329622	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs329623	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs329624	0.80[EUR][1000 genomes]
rs329625	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs329626	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34593	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34609	0.80[EUR][1000 genomes]
rs34613	0.80[EUR][1000 genomes]
rs34614	0.88[EUR][1000 genomes]
rs34616	0.80[EUR][1000 genomes]
rs34617	0.80[EUR][1000 genomes]
rs34621	0.88[EUR][1000 genomes]
rs34624	0.89[EUR][1000 genomes]
rs34625	0.81[EUR][1000 genomes]
rs34636	0.88[EUR][1000 genomes]
rs34637	0.88[EUR][1000 genomes]
rs34639	0.91[EUR][1000 genomes]
rs34644	0.91[EUR][1000 genomes]
rs35948426	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs39661	0.88[EUR][1000 genomes]
rs40084	0.91[EUR][1000 genomes]
rs4141502	0.89[EUR][1000 genomes]
rs4235483	0.86[EUR][1000 genomes]
rs4647102	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4647138	0.86[EUR][1000 genomes]
rs4647139	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4647162	0.82[EUR][1000 genomes]
rs4699969	0.81[EUR][1000 genomes]
rs56409036	0.97[EUR][1000 genomes]
rs6878124	0.89[EUR][1000 genomes]
rs6886481	0.89[EUR][1000 genomes]
rs723276	0.89[EUR][1000 genomes]
rs7701839	0.86[EUR][1000 genomes]
rs810883	0.89[EUR][1000 genomes]
rs976581	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv881713	chr5:60116613-60305125	Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv598305	chr5:60116613-60308836	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv881714	chr5:60116613-60313015	Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	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
9	nsv598307	chr5:60129361-60308836	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv881716	chr5:60129361-60313015	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv598310	chr5:60135985-60308836	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv598311	chr5:60136626-60308836	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv520871	chr5:60141245-60320157	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	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
17	nsv598312	chr5:60147754-60313015	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv881718	chr5:60147754-60313015	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	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
20	nsv933573	chr5:60224875-60309751	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv881721	chr5:60232646-60344399	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	nsv933769	chr5:60240706-60309751	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	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
24	nsv518695	chr5:60266875-60329624	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs162247	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60266200-60317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60287200-60290400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:60288600-60290200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr5:60288600-60290200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
5	chr5:60288600-60290200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:60288600-60290200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:60288600-60290200	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr5:60288600-60290400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:60288600-60290400	Enhancers	Left Ventricle	heart
10	chr5:60288800-60290200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr5:60288800-60290200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:60288800-60290200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:60288800-60290200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:60288800-60290200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:60288800-60290200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:60288800-60290200	Enhancers	Aorta	Aorta
17	chr5:60288800-60290200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
18	chr5:60288800-60290200	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr5:60288800-60290200	ZNF genes & repeats	Fetal Stomach	stomach
20	chr5:60288800-60290400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr5:60288800-60290400	ZNF genes & repeats	Lung	lung
22	chr5:60288800-60290400	Enhancers	Right Atrium	heart
23	chr5:60288800-60290400	Enhancers	Right Ventricle	heart
24	chr5:60288800-60290400	ZNF genes & repeats	Spleen	Spleen
25	chr5:60288800-60290800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
26	chr5:60288800-60291200	ZNF genes & repeats	Fetal Brain Female	brain
27	chr5:60289200-60290800	Weak transcription	Hela-S3	cervix
28	chr5:60289400-60290200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:60289400-60290200	Enhancers	Pancreas	Pancrea
30	chr5:60289400-60292400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:60289400-60293000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:60289400-60293200	Weak transcription	Primary T cells from cord blood	blood
33	chr5:60289400-60294600	Weak transcription	HepG2	liver
34	chr5:60289400-60295200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:60289600-60290600	Weak transcription	Fetal Lung	lung
36	chr5:60289600-60296400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:60289800-60290200	Weak transcription	Brain Angular Gyrus	brain
38	chr5:60289800-60290200	Genic enhancers	Gastric	stomach
39	chr5:60289800-60290400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:60289800-60290400	Enhancers	Psoas Muscle	Psoas
41	chr5:60289800-60291800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:60289800-60292000	Weak transcription	Esophagus	oesophagus
43	chr5:60289800-60295200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:60290000-60290200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:60290000-60291800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:60290000-60292200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:60290000-60296400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr5:60290000-60296400	Weak transcription	NHEK	skin
49	chr5:60290000-60297000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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