Variant report

Variant	rs1862539
Chromosome Location	chr5:57453246-57453247
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr5:57453146-57453526	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57451627..57453981-chr5:57754355..57756804,3	MCF-7	breast:

Variant related genes	Relation type
PGAM1P1	TF binding region
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1035475	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10472035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10472036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13155421	1.00[AFR][1000 genomes]
rs13168168	1.00[AFR][1000 genomes]
rs13168414	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13170721	1.00[AFR][1000 genomes]
rs13185712	1.00[AFR][1000 genomes]
rs13187650	1.00[ASN][1000 genomes]
rs1473200	1.00[ASN][1000 genomes]
rs1549243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16887923	1.00[AFR][1000 genomes]
rs17369645	1.00[AFR][1000 genomes]
rs17433525	1.00[AFR][1000 genomes]
rs17750857	1.00[AFR][1000 genomes]
rs17750946	1.00[AFR][1000 genomes]
rs17751024	1.00[AFR][1000 genomes]
rs1981838	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1981839	1.00[ASN][1000 genomes]
rs2194195	1.00[ASN][1000 genomes]
rs2216678	1.00[ASN][1000 genomes]
rs2216679	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2216683	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216685	1.00[ASN][1000 genomes]
rs2860439	1.00[ASN][1000 genomes]
rs2910567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2910569	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2910571	0.91[ASN][1000 genomes]
rs2910573	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2910593	1.00[ASN][1000 genomes]
rs2910594	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2910600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2910601	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2910605	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2910611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2910612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2961999	1.00[ASN][1000 genomes]
rs2962021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2962024	0.87[ASN][1000 genomes]
rs2964173	1.00[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2964184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2964208	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2964209	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34357926	1.00[AFR][1000 genomes]
rs34969852	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35132533	1.00[AFR][1000 genomes]
rs35629187	1.00[AFR][1000 genomes]
rs4340877	1.00[AFR][1000 genomes]
rs58405952	1.00[AFR][1000 genomes]
rs71624189	1.00[AFR][1000 genomes]
rs71624191	1.00[AFR][1000 genomes]
rs988697	1.00[ASN][1000 genomes]
rs989579	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033051	chr5:57380218-57471801	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57447200-57457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:57451000-57454000	Enhancers	Fetal Brain Male	brain
3	chr5:57451000-57454200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:57451400-57453400	Enhancers	Brain Anterior Caudate	brain
5	chr5:57451400-57453600	Enhancers	NH-A	brain
6	chr5:57451400-57453800	Enhancers	HSMM	muscle
7	chr5:57451600-57453400	Enhancers	Fetal Brain Female	brain
8	chr5:57451800-57454000	Enhancers	HSMMtube	muscle
9	chr5:57452000-57453400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:57452000-57453400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:57452000-57453400	Flanking Active TSS	Brain Germinal Matrix	brain
12	chr5:57452000-57453400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr5:57452000-57453400	Enhancers	NHDF-Ad	bronchial
14	chr5:57452000-57453400	Enhancers	Osteobl	bone
15	chr5:57452000-57453600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:57452200-57453400	Enhancers	Adipose Nuclei	Adipose
17	chr5:57452200-57453400	Enhancers	Left Ventricle	heart
18	chr5:57452400-57453400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:57452400-57453400	Enhancers	Brain Cingulate Gyrus	brain
20	chr5:57452400-57453400	Enhancers	NHEK	skin
21	chr5:57452400-57453600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:57452400-57454000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:57452400-57454000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr5:57452600-57454000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:57452800-57453400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:57452800-57453400	Enhancers	GM12878-XiMat	blood
27	chr5:57453000-57454200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:57453000-57457000	Weak transcription	Pancreas	Pancrea
29	chr5:57453200-57453400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:57453200-57453600	Enhancers	Duodenum Smooth Muscle	Duodenum

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