Variant report

Variant	rs10002513
Chromosome Location	chr4:56984306-56984307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10001537	0.84[EUR][1000 genomes]
rs10015524	0.84[EUR][1000 genomes]
rs13121935	0.93[AFR][1000 genomes]
rs1531586	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045982	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28426986	0.96[AFR][1000 genomes]
rs28465616	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34771783	0.93[AFR][1000 genomes]
rs4142	0.96[AFR][1000 genomes]
rs4864568	0.93[AFR][1000 genomes]
rs6836927	0.93[AFR][1000 genomes]
rs6849646	0.93[AFR][1000 genomes]
rs73240536	1.00[ASN][1000 genomes]
rs9994190	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9994666	0.82[AFR][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	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
3	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
4	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
5	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
6	nsv1012036	chr4:56963544-57106642	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56952000-57024400	Weak transcription	Fetal Intestine Small	intestine
2	chr4:56978800-56987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:56979000-56984400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:56979000-56984600	Weak transcription	Brain Germinal Matrix	brain
5	chr4:56979000-56993800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:56979000-56993800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:56980600-56993800	Weak transcription	Fetal Lung	lung
8	chr4:56982000-56984400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:56982200-56986200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr4:56982400-56986400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:56982400-56993800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:56982800-56988200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:56983000-56986000	Weak transcription	Fetal Intestine Large	intestine
14	chr4:56983600-56984800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:56984200-56984400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:56984200-56984600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:56984200-56984800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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