Variant report

Variant	rs1047959
Chromosome Location	chr4:53739856-53739857
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10001855	0.95[ASN][1000 genomes]
rs10008073	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs10014464	0.86[ASN][1000 genomes]
rs10032190	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1043975	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10866413	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11930907	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11934293	0.86[ASN][1000 genomes]
rs11940297	0.87[ASN][1000 genomes]
rs11941562	0.88[ASN][1000 genomes]
rs1483685	0.86[ASN][1000 genomes]
rs1483686	0.81[JPT][hapmap]
rs17082081	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17082143	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17082147	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1963003	0.86[ASN][1000 genomes]
rs2003198	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017237	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2046364	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2062253	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2200226	0.93[ASN][1000 genomes]
rs2279334	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2306601	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2411281	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28419463	0.85[ASN][1000 genomes]
rs28704139	0.86[ASN][1000 genomes]
rs2898681	0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs301119	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs301123	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs301135	0.85[JPT][hapmap]
rs4864679	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4864681	0.88[ASN][1000 genomes]
rs4864682	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4864683	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4864685	0.84[EUR][1000 genomes]
rs4864688	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864690	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864691	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59649036	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61268502	0.91[ASN][1000 genomes]
rs62336785	0.86[ASN][1000 genomes]
rs62336790	0.87[EUR][1000 genomes]
rs62336791	0.90[ASN][1000 genomes]
rs62336792	0.88[ASN][1000 genomes]
rs62336794	0.96[ASN][1000 genomes]
rs62336795	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62336823	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6833096	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839084	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852148	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73143042	0.86[ASN][1000 genomes]
rs8287	1.00[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs900607	0.92[ASN][1000 genomes]
rs922932	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs922933	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs936690	0.85[MEX][hapmap]
rs962416	0.85[MEX][hapmap]
rs9646	0.92[ASN][1000 genomes]
rs9993034	0.88[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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
2	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
3	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
5	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:53729600-53742200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:53730000-53743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:53731400-53751000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:53732400-53750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:53732400-53755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:53732800-53749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:53733000-53767800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr4:53733200-53759000	Weak transcription	Osteobl	bone
14	chr4:53733600-53740400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:53733600-53750200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:53734000-53749200	Weak transcription	Aorta	Aorta
17	chr4:53734200-53742200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:53734200-53760800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:53735000-53740200	Weak transcription	Fetal Kidney	kidney
21	chr4:53735000-53770200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:53735200-53755200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:53735200-53778000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:53735400-53742000	Weak transcription	Dnd41	blood
25	chr4:53735600-53740400	Weak transcription	Lung	lung
26	chr4:53735600-53751600	Weak transcription	Spleen	Spleen
27	chr4:53735800-53740000	Weak transcription	Pancreas	Pancrea
28	chr4:53735800-53772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:53736000-53740400	Weak transcription	Right Ventricle	heart
30	chr4:53736000-53750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:53736000-53752600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:53736200-53740000	Weak transcription	Fetal Brain Female	brain
33	chr4:53736200-53758800	Weak transcription	NHLF	lung
34	chr4:53736400-53744000	Weak transcription	Fetal Brain Male	brain
35	chr4:53736400-53746800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:53736400-53749600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:53736400-53752200	Weak transcription	Adipose Nuclei	Adipose
38	chr4:53736600-53747000	Weak transcription	HSMM	muscle
39	chr4:53736600-53749000	Weak transcription	HSMMtube	muscle
40	chr4:53736600-53759600	Weak transcription	Ovary	ovary
41	chr4:53736600-53785600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:53736800-53743000	Weak transcription	Fetal Stomach	stomach
43	chr4:53736800-53743200	Weak transcription	Brain Germinal Matrix	brain
44	chr4:53736800-53750800	Weak transcription	Brain Angular Gyrus	brain
45	chr4:53737000-53741200	Strong transcription	Primary T cells from cord blood	blood
46	chr4:53737200-53740200	Weak transcription	Psoas Muscle	Psoas
47	chr4:53737200-53750600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:53737200-53751200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:53737200-53779200	Weak transcription	Gastric	stomach
50	chr4:53737400-53740000	Weak transcription	Colon Smooth Muscle	Colon

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