Variant report

Variant	rs2253464
Chromosome Location	chr2:30966687-30966688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12052219	0.86[CHB][hapmap]
rs1967561	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2253243	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs561956	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv873770	chr2:30952987-30984850	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv520269	chr2:30958137-30988375	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2253464	CAD	cis	parietal	SCAN
rs2253464	LCLAT1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30940600-30969600	Weak transcription	Stomach Mucosa	stomach
2	chr2:30957000-30969800	Weak transcription	Fetal Intestine Large	intestine
3	chr2:30960400-30980000	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:30961600-30978400	Weak transcription	Pancreas	Pancrea
5	chr2:30962000-30970200	Weak transcription	Brain Substantia Nigra	brain
6	chr2:30962600-30967600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:30963600-30969600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:30964000-30970600	Strong transcription	Gastric	stomach
9	chr2:30964400-30969000	Strong transcription	Fetal Intestine Small	intestine
10	chr2:30964400-30978600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:30965400-30968800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr2:30965600-30967200	Weak transcription	Fetal Stomach	stomach
13	chr2:30965800-30999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:30966000-30967400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:30966000-30967400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:30966000-30967600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:30966000-30970000	Weak transcription	Colonic Mucosa	Colon
18	chr2:30966000-30970200	Weak transcription	Esophagus	oesophagus

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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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