Variant report

Variant	rs4947641
Chromosome Location	chr7:50489038-50489039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11763774	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11764792	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11770117	0.90[EUR][1000 genomes]
rs12154303	0.98[EUR][1000 genomes]
rs12533940	0.89[EUR][1000 genomes]
rs12670555	0.89[EUR][1000 genomes]
rs12718910	0.89[EUR][1000 genomes]
rs12719019	0.94[EUR][1000 genomes]
rs12719030	0.98[EUR][1000 genomes]
rs12719056	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4947827	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6964823	0.85[EUR][1000 genomes]
rs6969942	0.89[EUR][1000 genomes]
rs6978646	0.89[EUR][1000 genomes]
rs730092	0.89[YRI][hapmap]
rs7789635	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv515738	chr7:50476109-50494207	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4947641	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs4947641	FIGNL1	cis	Artery Tibial	GTEx
rs4947641	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs4947641	FIGNL1	cis	lung	GTEx
rs4947641	FIGNL1	cis	Esophagus Muscularis	GTEx
rs4947641	FIGNL1	cis	Nerve Tibial	GTEx
rs4947641	FIGNL1	Cis_1M	lymphoblastoid	RTeQTL
rs4947641	FIGNL1	cis	Thyroid	GTEx
rs4947641	FIGNL1	cis	Esophagus Mucosa	GTEx
rs4947641	FIGNL1	cis	Artery Aorta	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50485000-50490800	Weak transcription	Spleen	Spleen
2	chr7:50485400-50490400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:50486200-50513200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:50486400-50491600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr7:50486600-50495000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:50486800-50491400	Weak transcription	Fetal Thymus	thymus
7	chr7:50488000-50489800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr7:50488200-50489400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr7:50488400-50489200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr7:50488400-50489600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:50488600-50489400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:50488600-50489800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr7:50488800-50489400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr7:50488800-50489400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:50489000-50489200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr7:50489000-50489400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:50489000-50489400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:50489000-50489800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:50489000-50490200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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