Variant report

Variant	rs1451375
Chromosome Location	chr7:50622712-50622713
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10229102	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10229369	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10247443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249420	0.95[JPT][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs10250513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265930	0.95[JPT][hapmap]
rs10271341	0.82[MKK][hapmap]
rs10276473	0.87[MKK][hapmap]
rs10278338	0.81[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10499695	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs11238214	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs11489734	0.89[GIH][hapmap];0.85[TSI][hapmap]
rs11575320	0.82[MKK][hapmap]
rs11974297	0.87[CHB][hapmap];0.81[CHD][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1451373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[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];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470747	0.93[JPT][hapmap];0.89[YRI][hapmap]
rs17133878	0.91[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1966839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329340	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]
rs2329341	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329371	0.87[MKK][hapmap]
rs3779074	0.81[JPT][hapmap]
rs3779078	0.86[MKK][hapmap]
rs3829897	0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs4452748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947644	0.83[CHB][hapmap];0.83[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6962356	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]
rs6969081	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]
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];0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs7803788	0.95[JPT][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs7803903	0.86[AFR][1000 genomes]
rs921450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[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

Variant related diseases (count:1)

Disease	PMID	Source
Malaria	19465909	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1451375	FIGNL1	cis	lung	GTEx
rs1451375	FIGNL1	cis	parietal	SCAN
rs1451375	FIGNL1	cis	cerebellum	SCAN

Chromatin state (count:23 , 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	chr7:50620800-50635600	Weak transcription	Lung	lung
11	chr7:50621000-50623600	Weak transcription	Gastric	stomach
12	chr7:50621600-50622800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:50621600-50624200	Enhancers	Duodenum Mucosa	Duodenum
14	chr7:50621800-50624800	Enhancers	Placenta	Placenta
15	chr7:50621800-50627000	Enhancers	Pancreas	Pancrea
16	chr7:50622000-50622800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:50622000-50624200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:50622000-50624600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr7:50622000-50624600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:50622400-50622800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:50622400-50623000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:50622400-50625000	Enhancers	Small Intestine	intestine
23	chr7:50622600-50622800	Enhancers	Esophagus	oesophagus

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