Variant report

Variant	rs12404798
Chromosome Location	chr1:161945026-161945027
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10799979	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs10917946	0.82[CEU][hapmap]
rs10918004	0.81[AMR][1000 genomes]
rs10918124	0.82[ASN][1000 genomes]
rs1135983	0.80[CHB][hapmap]
rs1136046	0.80[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11582699	0.99[ASN][1000 genomes]
rs12023191	0.82[ASN][1000 genomes]
rs12025202	0.82[ASN][1000 genomes]
rs12025560	0.81[AMR][1000 genomes]
rs12028953	0.81[AMR][1000 genomes]
rs12029726	0.81[AMR][1000 genomes]
rs12030395	0.96[JPT][hapmap]
rs12032355	0.81[AMR][1000 genomes]
rs12032568	0.83[ASN][1000 genomes]
rs12033967	0.84[ASN][1000 genomes]
rs12034541	0.83[ASN][1000 genomes]
rs12036425	0.84[ASN][1000 genomes]
rs12036441	0.81[AMR][1000 genomes]
rs12040518	0.84[ASN][1000 genomes]
rs12040523	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12043145	0.81[ASN][1000 genomes]
rs12044770	0.81[AMR][1000 genomes]
rs12048680	0.82[ASN][1000 genomes]
rs12402354	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12403862	0.81[AMR][1000 genomes]
rs12404636	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12405111	0.82[CEU][hapmap]
rs12410839	0.81[ASN][1000 genomes]
rs1394068	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs1394069	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs1553443	0.82[CEU][hapmap]
rs16860777	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16863838	0.81[AMR][1000 genomes]
rs2070150	0.82[CEU][hapmap]
rs2070151	0.82[CEU][hapmap]
rs2089083	0.81[CHB][hapmap]
rs2271012	0.82[CEU][hapmap]
rs2271013	0.82[CEU][hapmap]
rs2340823	0.82[CEU][hapmap]
rs2341469	0.83[ASN][1000 genomes]
rs2341473	0.84[ASN][1000 genomes]
rs2341474	0.84[ASN][1000 genomes]
rs2341476	0.84[ASN][1000 genomes]
rs2341477	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2490432	0.99[ASN][1000 genomes]
rs2499842	0.98[ASN][1000 genomes]
rs2880056	0.80[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3820489	0.82[CEU][hapmap];0.96[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4147177	0.82[ASN][1000 genomes]
rs4147178	0.82[ASN][1000 genomes]
rs4233379	0.84[ASN][1000 genomes]
rs4278352	0.84[ASN][1000 genomes]
rs4625257	0.84[ASN][1000 genomes]
rs4657116	0.82[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4657117	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4657118	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4657120	0.82[CEU][hapmap];0.81[CHB][hapmap];0.96[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55741033	0.84[ASN][1000 genomes]
rs56085642	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56310275	0.81[AMR][1000 genomes]
rs6427634	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6427635	0.83[ASN][1000 genomes]
rs6427636	0.83[ASN][1000 genomes]
rs6427637	0.83[ASN][1000 genomes]
rs6687850	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6695284	0.81[AMR][1000 genomes]
rs7412625	0.84[ASN][1000 genomes]
rs7511775	0.81[ASN][1000 genomes]
rs7513427	0.82[ASN][1000 genomes]
rs7519012	0.84[ASN][1000 genomes]
rs7523416	0.82[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7530408	0.84[ASN][1000 genomes]
rs7530997	0.82[CEU][hapmap]
rs7532457	0.81[AMR][1000 genomes]
rs7534981	0.84[CHB][hapmap]
rs7535349	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs7537054	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7545293	0.82[CEU][hapmap];0.96[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs955852	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv464206	chr1:161798239-162067447	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv470744	chr1:161798239-162067447	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS 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	15 gene(s)	inside rSNPs	diseases
4	nsv548077	chr1:161798239-162067447	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1007108	chr1:161925814-162002917	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv831747	chr1:161926367-162103311	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv548078	chr1:161941219-161980502	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161904800-161956600	Weak transcription	Fetal Brain Male	brain
2	chr1:161932400-161955400	Weak transcription	Brain Substantia Nigra	brain
3	chr1:161933600-161953400	Weak transcription	HSMMtube	muscle
4	chr1:161937600-161954800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:161939200-161946000	Enhancers	Fetal Muscle Leg	muscle
6	chr1:161939200-161956600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:161940800-161952200	Weak transcription	Aorta	Aorta
8	chr1:161942200-161945200	Enhancers	Colon Smooth Muscle	Colon
9	chr1:161942200-161945200	Enhancers	Right Ventricle	heart
10	chr1:161942200-161951000	Weak transcription	Lung	lung
11	chr1:161942400-161945200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:161943000-161951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:161944000-161945200	Enhancers	HepG2	liver
14	chr1:161944200-161953800	Weak transcription	Esophagus	oesophagus
15	chr1:161944400-161946000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:161944400-161951800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:161944400-161952200	Weak transcription	NHDF-Ad	bronchial
18	chr1:161944400-161953400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:161944400-161953600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:161944400-161964000	Weak transcription	Ovary	ovary
21	chr1:161944600-161952200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:161944600-161953400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:161944600-161953400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:161945000-161950600	Weak transcription	Adipose Nuclei	Adipose

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