Variant report

Variant	rs10008254
Chromosome Location	chr4:56961449-56961450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10013329	1.00[JPT][hapmap]
rs10030394	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10517368	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11723545	0.83[AMR][1000 genomes]
rs11732604	0.94[EUR][1000 genomes]
rs11735331	0.94[EUR][1000 genomes]
rs2412729	0.94[EUR][1000 genomes]
rs2611815	0.94[EUR][1000 genomes]
rs2611816	0.94[EUR][1000 genomes]
rs2702331	1.00[JPT][hapmap]
rs2702348	1.00[JPT][hapmap]
rs28392731	0.83[AMR][1000 genomes]
rs28603237	0.83[AMR][1000 genomes]
rs41335053	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv999328	chr4:56942917-57041586	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1007114	chr4:56942917-57055381	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56945600-56965200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:56948800-56972200	Weak transcription	Fetal Stomach	stomach
3	chr4:56949000-56965200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:56952000-56961600	Weak transcription	Fetal Brain Female	brain
5	chr4:56952000-57024400	Weak transcription	Fetal Intestine Small	intestine
6	chr4:56952600-56963200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:56952600-56965200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:56952800-56968400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:56952800-56978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:56953000-56965200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:56953600-56965200	Weak transcription	Brain Germinal Matrix	brain
12	chr4:56955800-56963800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:56956800-56961600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr4:56957600-56971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:56961200-56962400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:56961400-56961800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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