Variant report

Variant	rs4452748
Chromosome Location	chr7:50625056-50625057
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10229102	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10229369	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10247443	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249420	0.95[JPT][hapmap];0.93[MKK][hapmap];0.91[YRI][hapmap]
rs10250513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[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];0.87[EUR][1000 genomes]
rs10499695	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs11238214	0.88[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11489734	0.89[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11575320	0.82[MKK][hapmap]
rs11974297	0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12665904	0.80[EUR][1000 genomes]
rs1451373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[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];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451375	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]
rs1470747	0.93[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs17133878	0.91[CHB][hapmap];0.91[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329340	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]
rs2329341	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.83[EUR][1000 genomes]
rs4947644	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs55738142	0.83[EUR][1000 genomes]
rs56233242	0.80[EUR][1000 genomes]
rs6593010	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs6949897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[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];0.89[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];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73125288	0.83[EUR][1000 genomes]
rs73125290	0.83[EUR][1000 genomes]
rs7779110	0.82[AFR][1000 genomes]
rs7786398	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs7803440	1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes]
rs7803788	0.95[JPT][hapmap];0.95[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs7803903	0.88[AFR][1000 genomes]
rs921450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.98[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];1.00[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4452748	FIGNL1	cis	parietal	SCAN
rs4452748	FIGNL1	cis	lung	GTEx
rs4452748	FIGNL1	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr7:50620800-50635600	Weak transcription	Lung	lung
6	chr7:50621800-50627000	Enhancers	Pancreas	Pancrea
7	chr7:50623000-50626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:50623600-50625400	Enhancers	Fetal Stomach	stomach
9	chr7:50623600-50625600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:50623600-50625600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:50623800-50626800	Enhancers	Ovary	ovary
12	chr7:50624000-50625400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr7:50624000-50625600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:50624200-50625200	Bivalent Enhancer	HSMMtube	muscle
15	chr7:50624200-50625400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr7:50624400-50625600	Enhancers	Brain Germinal Matrix	brain
17	chr7:50624400-50625600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr7:50624400-50626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:50624400-50626400	Enhancers	Fetal Intestine Small	intestine
20	chr7:50624600-50625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:50624600-50625600	Enhancers	Fetal Lung	lung
22	chr7:50624600-50626000	Weak transcription	Stomach Mucosa	stomach
23	chr7:50624600-50631800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr7:50624800-50625200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:50624800-50626200	Weak transcription	Liver	Liver
26	chr7:50625000-50626000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:50625000-50626600	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr7:50625000-50628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:50625000-50628600	Weak transcription	Small Intestine	intestine

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