Variant report

Variant	rs11238131
Chromosome Location	chr7:50538589-50538590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11575520	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3757472	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4329234	0.81[YRI][hapmap]
rs4397355	0.80[EUR][1000 genomes]
rs4470989	0.93[EUR][1000 genomes]
rs4947535	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7780360	0.84[EUR][1000 genomes]
rs7785224	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7803247	0.91[JPT][hapmap];0.81[MKK][hapmap]
rs7809477	0.86[AMR][1000 genomes];0.94[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	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11238131	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs11238131	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs11238131	FIGNL1	cis	Nerve Tibial	GTEx
rs11238131	FIGNL1	cis	Thyroid	GTEx
rs11238131	FIGNL1	cis	lung	GTEx
rs11238131	FIGNL1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535800-50539000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr7:50535800-50540800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:50535800-50546800	Weak transcription	Pancreas	Pancrea
4	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:50536000-50542800	Weak transcription	Colonic Mucosa	Colon
6	chr7:50536200-50541400	Weak transcription	HepG2	liver
7	chr7:50536200-50542200	Strong transcription	Fetal Intestine Small	intestine
8	chr7:50536200-50545400	Weak transcription	Right Atrium	heart
9	chr7:50536400-50541400	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:50536400-50541600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:50536400-50541800	Strong transcription	Fetal Intestine Large	intestine
12	chr7:50536600-50543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:50537800-50538600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr7:50538200-50538800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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