Variant report

Variant	rs2253121
Chromosome Location	chr2:30969801-30969802
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13414988	0.82[CHB][hapmap]
rs13428030	0.82[CHB][hapmap]
rs1474194	0.86[ASW][hapmap];0.84[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs1967560	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1967561	0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs2139592	0.84[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2253243	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2253464	0.87[MEX][hapmap]
rs2280404	0.82[CHB][hapmap]
rs2926304	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs545997	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs561956	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9679326	0.82[CHB][hapmap]

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	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
4	nsv456019	chr2:30968228-30984850	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv581267	chr2:30968228-30984850	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv961023	chr2:30968718-30969805	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2253121	AGBL5	cis	parietal	SCAN
rs2253121	LCLAT1	cis	parietal	SCAN
rs2253121	MPV17	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30960400-30980000	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:30961600-30978400	Weak transcription	Pancreas	Pancrea
3	chr2:30962000-30970200	Weak transcription	Brain Substantia Nigra	brain
4	chr2:30964000-30970600	Strong transcription	Gastric	stomach
5	chr2:30964400-30978600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:30965800-30999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:30966000-30970000	Weak transcription	Colonic Mucosa	Colon
8	chr2:30966000-30970200	Weak transcription	Esophagus	oesophagus
9	chr2:30967400-30978800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:30968200-30985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:30968600-30970400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:30968600-30975000	Weak transcription	Fetal Stomach	stomach
13	chr2:30968800-30970000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:30968800-30970800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:30969600-30970800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr2:30969600-30971000	Enhancers	Stomach Mucosa	stomach
17	chr2:30969800-30970200	Enhancers	Fetal Intestine Small	intestine
18	chr2:30969800-30970600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:30969800-30970800	Enhancers	Fetal Intestine Large	intestine

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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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