Variant report

Variant	rs6969081
Chromosome Location	chr7:50624505-50624506
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10229102	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10229369	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10247443	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10250513	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10278338	0.92[CEU][hapmap];0.85[GIH][hapmap];0.86[EUR][1000 genomes]
rs10499695	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs11238214	0.80[CEU][hapmap]
rs11974297	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12718674	0.85[ASN][1000 genomes]
rs1451373	0.80[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1451374	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1451375	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17133878	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966839	0.83[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2329340	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2329341	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2329342	0.81[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3829897	0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs4452748	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4947644	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs55738142	0.81[EUR][1000 genomes]
rs6593010	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6949897	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6962356	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]
rs73125288	0.81[EUR][1000 genomes]
rs73125290	0.81[EUR][1000 genomes]
rs921450	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs921451	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	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
rs6969081	FIGNL1	cis	Nerve Tibial	GTEx
rs6969081	FIGNL1	cis	lung	GTEx
rs6969081	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs6969081	FIGNL1	cis	parietal	SCAN
rs6969081	FIGNL1	cis	cerebellum	SCAN

Chromatin state (count:37 , 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	chr7:50619400-50628200	Enhancers	HepG2	liver
4	chr7:50619600-50627800	Enhancers	Fetal Intestine Large	intestine
5	chr7:50620400-50624600	Weak transcription	Fetal Lung	lung
6	chr7:50620600-50625000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:50620800-50635600	Weak transcription	Lung	lung
8	chr7:50621800-50624800	Enhancers	Placenta	Placenta
9	chr7:50621800-50627000	Enhancers	Pancreas	Pancrea
10	chr7:50622000-50624600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:50622000-50624600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:50622400-50625000	Enhancers	Small Intestine	intestine
13	chr7:50623000-50626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:50623400-50625000	Enhancers	Stomach Smooth Muscle	stomach
15	chr7:50623600-50625400	Enhancers	Fetal Stomach	stomach
16	chr7:50623600-50625600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:50623600-50625600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:50623800-50624800	Enhancers	Liver	Liver
19	chr7:50623800-50626800	Enhancers	Ovary	ovary
20	chr7:50624000-50624800	Enhancers	Colon Smooth Muscle	Colon
21	chr7:50624000-50625400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr7:50624000-50625600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:50624200-50624600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr7:50624200-50624600	Enhancers	Adipose Nuclei	Adipose
25	chr7:50624200-50624600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr7:50624200-50624600	Enhancers	Stomach Mucosa	stomach
27	chr7:50624200-50624800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:50624200-50625000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:50624200-50625000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr7:50624200-50625200	Bivalent Enhancer	HSMMtube	muscle
31	chr7:50624200-50625400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr7:50624400-50624600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr7:50624400-50625000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr7:50624400-50625600	Enhancers	Brain Germinal Matrix	brain
35	chr7:50624400-50625600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr7:50624400-50626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:50624400-50626400	Enhancers	Fetal Intestine Small	intestine

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