Variant report

Variant	rs6962356
Chromosome Location	chr7:50621941-50621942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10229102	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10229369	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10247443	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10250513	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10499695	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11974297	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12718674	0.84[ASN][1000 genomes]
rs1451373	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1451374	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1451375	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17133878	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1966839	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2329340	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2329341	0.95[CEU][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2329342	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3829897	0.81[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs4452748	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4947644	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6949897	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6969081	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921450	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs921451	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv429750	chr7:50603534-50622712	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv429751	chr7:50607353-50622712	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1032882	chr7:50611138-50775257	Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv538834	chr7:50611138-50775257	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6962356	FIGNL1	cis	Nerve Tibial	GTEx
rs6962356	FIGNL1	cis	Thyroid	GTEx
rs6962356	FIGNL1	cis	parietal	SCAN
rs6962356	FIGNL1	cis	lung	GTEx
rs6962356	FIGNL1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50601600-50631400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:50611000-50631800	Weak transcription	Colonic Mucosa	Colon
3	chr7:50611600-50623800	Weak transcription	Liver	Liver
4	chr7:50619400-50624400	Genic enhancers	Fetal Intestine Small	intestine
5	chr7:50619400-50628200	Enhancers	HepG2	liver
6	chr7:50619600-50627800	Enhancers	Fetal Intestine Large	intestine
7	chr7:50620400-50624600	Weak transcription	Fetal Lung	lung
8	chr7:50620600-50624200	Weak transcription	Stomach Mucosa	stomach
9	chr7:50620600-50625000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:50620800-50622400	Weak transcription	Esophagus	oesophagus
11	chr7:50620800-50635600	Weak transcription	Lung	lung
12	chr7:50621000-50623600	Weak transcription	Gastric	stomach
13	chr7:50621600-50622000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:50621600-50622000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:50621600-50622000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:50621600-50622200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:50621600-50622800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:50621600-50624200	Enhancers	Duodenum Mucosa	Duodenum
19	chr7:50621800-50624800	Enhancers	Placenta	Placenta
20	chr7:50621800-50627000	Enhancers	Pancreas	Pancrea

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