Variant report

Variant	rs2523974
Chromosome Location	chr6:30089428-30089429
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1123966	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1419675	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1967	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2021723	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021731	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107195	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2107202	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2244066	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2257914	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517591	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523733	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2523734	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2523995	0.82[EUR][1000 genomes]
rs2844798	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv601476	chr6:30085838-30091311	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2523974	HIST1H2BN	cis	parietal	SCAN
rs2523974	ZKSCAN4	cis	cerebellum	SCAN
rs2523974	HIST1H4F	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30082400-30091000	Weak transcription	HepG2	liver
2	chr6:30086200-30092600	Enhancers	Fetal Intestine Small	intestine
3	chr6:30087400-30090600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:30087600-30089600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:30088000-30089800	Weak transcription	NHDF-Ad	bronchial
6	chr6:30089000-30092600	Enhancers	Fetal Intestine Large	intestine
7	chr6:30089200-30089800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
8	chr6:30089200-30090400	Enhancers	Colonic Mucosa	Colon
9	chr6:30089200-30092400	Enhancers	Hela-S3	cervix
10	chr6:30089400-30089600	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr6:30089400-30090600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr6:30089400-30091000	Enhancers	Stomach Mucosa	stomach
13	chr6:30089400-30092400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:30089400-30092600	Enhancers	Duodenum Mucosa	Duodenum

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Input of quick search could be:

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

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