Variant report

Variant	rs2329340
Chromosome Location	chr7:50620229-50620230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10229102	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10229369	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10247443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249420	0.95[JPT][hapmap];0.91[MKK][hapmap]
rs10250513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265930	0.95[JPT][hapmap]
rs10271341	0.84[MKK][hapmap];0.83[YRI][hapmap]
rs10276473	0.89[MKK][hapmap];0.87[YRI][hapmap]
rs10278338	0.81[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10499695	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs11238214	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs11489734	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs11575320	0.84[MKK][hapmap];0.83[YRI][hapmap]
rs11974297	0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1451373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470747	0.93[JPT][hapmap]
rs17133878	0.91[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1966839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329341	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329371	0.89[MKK][hapmap];0.87[YRI][hapmap]
rs3779074	0.81[JPT][hapmap]
rs3779078	0.88[MKK][hapmap];0.83[YRI][hapmap]
rs3807555	0.87[YRI][hapmap]
rs3829897	0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs4452748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947644	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs55738142	0.81[EUR][1000 genomes]
rs6593010	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs6949897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6962356	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]
rs6969081	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]
rs73125288	0.81[EUR][1000 genomes]
rs73125290	0.81[EUR][1000 genomes]
rs7786398	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs7803440	1.00[JPT][hapmap]
rs7803788	0.95[JPT][hapmap];0.93[MKK][hapmap]
rs921450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2329340	FIGNL1	cis	lung	GTEx
rs2329340	FIGNL1	cis	Thyroid	GTEx
rs2329340	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs2329340	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2329340	FIGNL1	cis	cerebellum	SCAN
rs2329340	FIGNL1	cis	parietal	SCAN

Chromatin state (count:13 , 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	chr7:50613000-50621600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:50619400-50620600	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr7:50619400-50624400	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:50619400-50628200	Enhancers	HepG2	liver
8	chr7:50619600-50620600	Enhancers	Stomach Mucosa	stomach
9	chr7:50619600-50621000	Enhancers	Gastric	stomach
10	chr7:50619600-50627800	Enhancers	Fetal Intestine Large	intestine
11	chr7:50620000-50620800	Enhancers	Esophagus	oesophagus
12	chr7:50620000-50620800	Enhancers	Lung	lung
13	chr7:50620000-50621000	Enhancers	Pancreas	Pancrea

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