Variant report

Variant	rs7790230
Chromosome Location	chr7:50522857-50522858
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10230307	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10230343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10232974	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10239496	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10243511	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1451373	0.85[JPT][hapmap]
rs1451376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060762	0.95[JPT][hapmap]
rs2305358	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3735275	0.95[JPT][hapmap]
rs3779074	0.81[JPT][hapmap]
rs4947437	0.95[AFR][1000 genomes]
rs4947510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947954	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947980	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6945253	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs896309	0.81[JPT][hapmap]
rs935795	0.93[EUR][1000 genomes];0.98[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7790230	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs7790230	FIGNL1	cis	Nerve Tibial	GTEx
rs7790230	FIGNL1	cis	Esophagus Muscularis	GTEx
rs7790230	FIGNL1	cis	Artery Tibial	GTEx
rs7790230	FIGNL1	cis	lung	GTEx
rs7790230	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs7790230	FIGNL1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50518800-50535400	Weak transcription	Pancreas	Pancrea
2	chr7:50518800-50535600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:50518800-50535600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:50518800-50535600	Weak transcription	HepG2	liver
5	chr7:50519000-50523400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:50519000-50523400	Weak transcription	Liver	Liver
7	chr7:50519000-50523400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:50519000-50523800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:50519000-50523800	Weak transcription	Fetal Intestine Small	intestine
10	chr7:50519000-50524400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:50519000-50529400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:50519200-50523400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr7:50519200-50524000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:50519200-50524000	Weak transcription	Fetal Intestine Large	intestine
15	chr7:50522600-50523000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:50522600-50525400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

Quick Search:

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

what's new

Quick links