Variant report

Variant	rs3807558
Chromosome Location	chr7:50571022-50571023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50570130..50572623-chr7:50573822..50576522,2	K562	blood:
2	chr7:50569843..50571376-chr7:50579895..50581810,2	K562	blood:
3	chr7:50565140..50566781-chr7:50570058..50572270,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10239830	0.89[EUR][1000 genomes]
rs10249420	0.88[GIH][hapmap]
rs10267323	0.91[EUR][1000 genomes]
rs10271341	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs10276473	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10277662	0.91[EUR][1000 genomes]
rs11238133	0.87[LWK][hapmap];0.90[MKK][hapmap]
rs11238134	0.86[YRI][hapmap]
rs11575320	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs11575463	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11761683	0.87[LWK][hapmap];0.90[MKK][hapmap];0.87[YRI][hapmap]
rs11772714	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12666409	0.81[GIH][hapmap]
rs12671474	0.91[EUR][1000 genomes]
rs1376524	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17733244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1807066	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060762	0.83[YRI][hapmap]
rs2060763	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2242042	0.84[EUR][1000 genomes]
rs2329371	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2876828	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2876829	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28889020	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3735273	0.82[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3735275	0.87[YRI][hapmap]
rs3779078	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs3807552	0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap]
rs3807555	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs3807556	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs4449741	0.80[AMR][1000 genomes]
rs6950777	0.91[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6963996	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs745042	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs745043	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7776816	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7785224	0.95[CHB][hapmap]
rs7790758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803440	0.82[CEU][hapmap]
rs7803788	0.88[GIH][hapmap]
rs7807335	0.81[GIH][hapmap]
rs880029	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896307	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs896309	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9942686	1.00[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3807558	FIGNL1	cis	Artery Tibial	GTEx
rs3807558	FIGNL1	cis	lung	GTEx
rs3807558	FIGNL1	cis	parietal	SCAN
rs3807558	FIGNL1	cis	lymphoblastoid	seeQTL
rs3807558	FIGNL1	cis	Heart Left Ventricle	GTEx
rs3807558	FIGNL1	cis	Nerve Tibial	GTEx
rs3807558	FIGNL1	cis	Thyroid	GTEx
rs3807558	FIGNL1	cis	cerebellum	SCAN
rs3807558	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs3807558	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50560800-50581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
6	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
7	chr7:50566400-50572600	Strong transcription	Fetal Intestine Large	intestine
8	chr7:50566800-50571400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr7:50568200-50574400	Enhancers	Fetal Muscle Leg	muscle
10	chr7:50568800-50571400	Enhancers	HMEC	breast
11	chr7:50569000-50592800	Weak transcription	HepG2	liver
12	chr7:50569400-50571200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:50569400-50572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:50569600-50571200	Enhancers	Fetal Stomach	stomach
15	chr7:50569600-50571200	Enhancers	Rectal Smooth Muscle	rectum
16	chr7:50569800-50571200	Enhancers	Fetal Muscle Trunk	muscle
17	chr7:50569800-50571200	Enhancers	Ovary	ovary
18	chr7:50569800-50571200	Enhancers	HSMMtube	muscle
19	chr7:50570000-50571200	Enhancers	Adipose Nuclei	Adipose
20	chr7:50570000-50571200	Enhancers	NHLF	lung
21	chr7:50570200-50571200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr7:50570200-50571200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr7:50570600-50571400	Enhancers	Colon Smooth Muscle	Colon
24	chr7:50570600-50572200	Enhancers	Psoas Muscle	Psoas
25	chr7:50570600-50572400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:50570600-50572800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:50570800-50571200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:50570800-50571200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:50570800-50571400	Enhancers	Muscle Satellite Cultured Cells	--
30	chr7:50570800-50571800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:50570800-50572000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr7:50570800-50572200	Weak transcription	Lung	lung
33	chr7:50570800-50573000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:50570800-50576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:50571000-50572200	Weak transcription	Left Ventricle	heart
36	chr7:50571000-50573200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:50571000-50573200	Enhancers	HSMM	muscle
38	chr7:50571000-50576000	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:50571000-50580200	Weak transcription	Pancreas	Pancrea
40	chr7:50571000-50582400	Weak transcription	Right Atrium	heart

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