Variant report

Variant	rs620913
Chromosome Location	chr1:47118067-47118068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10158678	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10159351	0.93[EUR][1000 genomes]
rs1025806	0.90[EUR][1000 genomes]
rs1048351	0.90[EUR][1000 genomes]
rs1048380	0.88[EUR][1000 genomes]
rs1075982	0.94[EUR][1000 genomes]
rs10789492	0.80[EUR][1000 genomes]
rs10789493	0.80[EUR][1000 genomes]
rs10890411	0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs10890412	0.93[JPT][hapmap]
rs10890416	0.82[EUR][1000 genomes]
rs11211334	0.92[JPT][hapmap]
rs11211338	0.92[EUR][1000 genomes]
rs11211340	0.88[JPT][hapmap]
rs11211341	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211344	0.93[EUR][1000 genomes]
rs11211346	0.88[EUR][1000 genomes]
rs11211354	0.80[EUR][1000 genomes]
rs1139758	0.94[EUR][1000 genomes]
rs1150064	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150068	0.94[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801316	0.91[EUR][1000 genomes]
rs11801419	0.86[EUR][1000 genomes]
rs11804665	0.94[EUR][1000 genomes]
rs12029031	0.86[JPT][hapmap]
rs12047537	0.94[EUR][1000 genomes]
rs12048954	0.92[JPT][hapmap]
rs12078635	0.93[EUR][1000 genomes]
rs12082387	0.86[EUR][1000 genomes]
rs12094663	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258000	0.84[EUR][1000 genomes]
rs1258002	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258004	0.82[AMR][1000 genomes]
rs1258052	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258053	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258054	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258056	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258059	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13417	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1440486	0.90[EUR][1000 genomes]
rs1440489	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17102352	0.94[EUR][1000 genomes]
rs17102355	0.94[EUR][1000 genomes]
rs17102473	0.87[EUR][1000 genomes]
rs1745377	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933933	0.94[EUR][1000 genomes]
rs1962900	0.90[EUR][1000 genomes]
rs2083486	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2119301	0.91[EUR][1000 genomes]
rs2218189	0.83[CHB][hapmap];0.93[EUR][1000 genomes]
rs2241862	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275380	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2289446	0.94[EUR][1000 genomes]
rs2289447	0.91[EUR][1000 genomes]
rs2304745	0.91[EUR][1000 genomes]
rs2405026	0.90[EUR][1000 genomes]
rs2405030	0.92[EUR][1000 genomes]
rs34932727	0.90[EUR][1000 genomes]
rs3737731	0.90[EUR][1000 genomes]
rs3766211	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766212	0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766214	0.93[EUR][1000 genomes]
rs3766215	0.91[EUR][1000 genomes]
rs3766217	0.90[EUR][1000 genomes]
rs3766219	0.83[CHB][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3766224	0.94[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4272563	0.92[EUR][1000 genomes]
rs4274009	0.89[EUR][1000 genomes]
rs4301586	0.91[EUR][1000 genomes]
rs4443838	0.94[EUR][1000 genomes]
rs55914029	0.88[EUR][1000 genomes]
rs56319728	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58185502	0.91[EUR][1000 genomes]
rs585257	0.94[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs594118	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs595813	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59881815	0.94[EUR][1000 genomes]
rs60173509	0.94[EUR][1000 genomes]
rs60675294	0.91[EUR][1000 genomes]
rs611468	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614486	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782563	0.90[EUR][1000 genomes]
rs61782564	0.90[EUR][1000 genomes]
rs61782568	0.91[EUR][1000 genomes]
rs61782590	0.80[EUR][1000 genomes]
rs61784001	0.94[EUR][1000 genomes]
rs61784002	0.94[EUR][1000 genomes]
rs61784003	0.92[EUR][1000 genomes]
rs618554	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618878	0.82[EUR][1000 genomes]
rs620431	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625507	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625590	0.94[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs637760	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638845	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6429607	0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6429608	0.84[EUR][1000 genomes]
rs6429609	0.87[EUR][1000 genomes]
rs6429610	0.81[EUR][1000 genomes]
rs647999	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666405	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667885	0.89[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669393	0.94[EUR][1000 genomes]
rs6670495	0.81[EUR][1000 genomes]
rs6671005	0.90[EUR][1000 genomes]
rs6671124	0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6688195	0.91[EUR][1000 genomes]
rs723334	0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723690	0.80[EUR][1000 genomes]
rs732539	0.92[EUR][1000 genomes]
rs7354865	0.91[EUR][1000 genomes]
rs7412469	0.91[EUR][1000 genomes]
rs744096	0.94[EUR][1000 genomes]
rs7519866	0.84[EUR][1000 genomes]
rs7532601	0.93[EUR][1000 genomes]
rs7534179	0.80[EUR][1000 genomes]
rs7541868	0.92[EUR][1000 genomes]
rs7553243	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs946320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs620913	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL
rs620913	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:47101800-47119000	Weak transcription	Colonic Mucosa	Colon
7	chr1:47101800-47121200	Weak transcription	HUVEC	blood vessel
8	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:47102400-47121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
11	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
12	chr1:47108200-47123400	Weak transcription	K562	blood
13	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
14	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
15	chr1:47109600-47123400	Weak transcription	NH-A	brain
16	chr1:47109600-47132600	Weak transcription	HMEC	breast
17	chr1:47109800-47123200	Weak transcription	HepG2	liver
18	chr1:47112200-47125600	Strong transcription	Liver	Liver
19	chr1:47112400-47126800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:47112800-47125400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:47112800-47125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:47113000-47124400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:47113600-47121800	Weak transcription	NHEK	skin
24	chr1:47113800-47118400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:47114600-47124600	Strong transcription	Fetal Thymus	thymus
26	chr1:47115000-47125200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:47115000-47125400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:47115400-47124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:47115600-47119000	Weak transcription	NHLF	lung
30	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:47115800-47121600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:47115800-47121800	Weak transcription	Psoas Muscle	Psoas
33	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
34	chr1:47116000-47118800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:47116000-47119000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:47116000-47119000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:47116000-47120400	Weak transcription	Gastric	stomach
38	chr1:47116000-47120600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:47116000-47121400	Weak transcription	Dnd41	blood
40	chr1:47116000-47121600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:47116000-47121800	Weak transcription	Right Ventricle	heart
42	chr1:47116000-47123800	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach
44	chr1:47116000-47130000	Weak transcription	Lung	lung
45	chr1:47116000-47130600	Weak transcription	Esophagus	oesophagus
46	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
47	chr1:47116200-47121600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:47116400-47118400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:47116400-47118600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:47116400-47119600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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