Variant report

Variant	rs2898681
Chromosome Location	chr4:53757000-53757001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10001855	0.94[ASN][1000 genomes]
rs10008073	0.81[CHB][hapmap]
rs10014464	0.83[ASN][1000 genomes]
rs1043975	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.90[ASN][1000 genomes]
rs1047959	0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs10866413	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11930907	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11934293	0.83[ASN][1000 genomes]
rs11940297	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11941562	0.85[ASN][1000 genomes]
rs1483685	0.83[ASN][1000 genomes]
rs1483686	0.81[JPT][hapmap]
rs17082081	0.86[JPT][hapmap]
rs17082143	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17082147	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1963003	0.83[ASN][1000 genomes]
rs2003198	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2017237	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046364	0.94[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2062253	0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.90[ASN][1000 genomes]
rs2200226	0.90[ASN][1000 genomes]
rs2279334	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.90[ASN][1000 genomes]
rs2306601	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];0.93[ASN][1000 genomes]
rs2411281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419463	0.83[ASN][1000 genomes]
rs28704139	0.83[ASN][1000 genomes]
rs301090	0.80[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	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4864681	0.85[ASN][1000 genomes]
rs4864682	0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[ASN][1000 genomes]
rs4864683	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4864688	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864690	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864691	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59649036	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61268502	0.89[ASN][1000 genomes]
rs62336785	0.83[ASN][1000 genomes]
rs62336791	0.88[ASN][1000 genomes]
rs62336792	0.86[ASN][1000 genomes]
rs62336794	0.93[ASN][1000 genomes]
rs62336795	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62336823	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833096	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852148	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73143042	0.83[ASN][1000 genomes]
rs8287	0.87[TSI][hapmap]
rs900607	0.93[ASN][1000 genomes]
rs922932	0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.85[ASN][1000 genomes]
rs922933	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9646	0.89[ASN][1000 genomes]
rs9993034	0.85[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

Variant related diseases (count:1)

Disease	PMID	Source
Optic nerve measurement (cup area)	20395239	GWAS catalog

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
2	chr4:53733000-53767800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr4:53733200-53759000	Weak transcription	Osteobl	bone
4	chr4:53734200-53760800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:53735000-53770200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:53735200-53778000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:53735800-53772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:53736200-53758800	Weak transcription	NHLF	lung
10	chr4:53736600-53759600	Weak transcription	Ovary	ovary
11	chr4:53736600-53785600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:53737200-53779200	Weak transcription	Gastric	stomach
13	chr4:53741000-53757400	Weak transcription	Pancreas	Pancrea
14	chr4:53741000-53757800	Weak transcription	Fetal Lung	lung
15	chr4:53741800-53757800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:53743400-53771000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:53743600-53758200	Weak transcription	Psoas Muscle	Psoas
18	chr4:53743600-53770200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:53744000-53758000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:53750200-53770000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:53750400-53769400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:53750600-53757000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:53750600-53769400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:53750800-53757200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:53751800-53760400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:53752800-53767000	Weak transcription	Thymus	Thymus
27	chr4:53753000-53757000	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:53753000-53758200	Weak transcription	Fetal Stomach	stomach
29	chr4:53753200-53760600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:53755400-53768000	Weak transcription	Primary B cells from cord blood	blood
31	chr4:53756000-53757200	Enhancers	NHEK	skin
32	chr4:53756000-53757400	Enhancers	NHDF-Ad	bronchial
33	chr4:53756000-53760000	Weak transcription	Primary T cells from cord blood	blood
34	chr4:53756000-53760800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:53756000-53761200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:53756600-53757200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:53756800-53757000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:53756800-53758400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:53757000-53758200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:53757000-53758200	Enhancers	Fetal Muscle Leg	muscle
41	chr4:53757000-53767200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:53757000-53781200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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