Variant report

Variant	rs880029
Chromosome Location	chr7:50569927-50569928
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50564851..50566745-chr7:50568557..50570240,2	K562	blood:
2	chr7:50569843..50571376-chr7:50579895..50581810,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10239830	0.88[EUR][1000 genomes]
rs10267323	0.90[EUR][1000 genomes]
rs10271341	0.90[EUR][1000 genomes]
rs10276473	0.82[EUR][1000 genomes]
rs10277662	0.90[EUR][1000 genomes]
rs11575320	0.90[EUR][1000 genomes]
rs11575463	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11772714	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12671474	0.90[EUR][1000 genomes]
rs1376524	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17733244	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1807066	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2060763	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2242042	0.84[EUR][1000 genomes]
rs2329371	0.82[EUR][1000 genomes]
rs2876828	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2876829	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28889020	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3735273	0.82[EUR][1000 genomes]
rs3779078	0.87[EUR][1000 genomes]
rs3807555	0.82[EUR][1000 genomes]
rs3807556	0.87[EUR][1000 genomes]
rs3807558	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4449741	0.82[AMR][1000 genomes]
rs6950777	0.82[EUR][1000 genomes]
rs6963996	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs745042	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs745043	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7776816	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7790758	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs896309	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9942686	0.90[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs880029	FIGNL1	cis	Thyroid	GTEx
rs880029	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs880029	FIGNL1	cis	Heart Left Ventricle	GTEx
rs880029	FIGNL1	cis	Nerve Tibial	GTEx
rs880029	FIGNL1	cis	Artery Tibial	GTEx
rs880029	FIGNL1	cis	lung	GTEx
rs880029	FIGNL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr7:50565200-50570000	Weak transcription	Left Ventricle	heart
4	chr7:50565200-50570200	Weak transcription	Lung	lung
5	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:50565400-50570000	Weak transcription	Pancreas	Pancrea
8	chr7:50565400-50570000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr7:50565400-50570000	Enhancers	Hela-S3	cervix
10	chr7:50565800-50570000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
12	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
13	chr7:50566400-50572600	Strong transcription	Fetal Intestine Large	intestine
14	chr7:50566800-50571400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr7:50568200-50574400	Enhancers	Fetal Muscle Leg	muscle
16	chr7:50568400-50570200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr7:50568800-50571400	Enhancers	HMEC	breast
18	chr7:50569000-50570400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:50569000-50570600	Weak transcription	Psoas Muscle	Psoas
20	chr7:50569000-50592800	Weak transcription	HepG2	liver
21	chr7:50569200-50570400	Enhancers	Colon Smooth Muscle	Colon
22	chr7:50569400-50570000	Enhancers	Stomach Smooth Muscle	stomach
23	chr7:50569400-50571000	Enhancers	Primary hematopoietic stem cells	blood
24	chr7:50569400-50571200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:50569400-50572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:50569600-50570200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr7:50569600-50570400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:50569600-50570600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:50569600-50570600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:50569600-50570800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:50569600-50571200	Enhancers	Fetal Stomach	stomach
32	chr7:50569600-50571200	Enhancers	Rectal Smooth Muscle	rectum
33	chr7:50569800-50570200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr7:50569800-50570200	Enhancers	NH-A	brain
35	chr7:50569800-50570400	Enhancers	HSMM	muscle
36	chr7:50569800-50570600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr7:50569800-50570800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:50569800-50570800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:50569800-50570800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr7:50569800-50570800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr7:50569800-50570800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:50569800-50570800	Enhancers	HUVEC	blood vessel
43	chr7:50569800-50570800	Enhancers	NHDF-Ad	bronchial
44	chr7:50569800-50570800	Enhancers	NHEK	skin
45	chr7:50569800-50571000	Enhancers	Aorta	Aorta
46	chr7:50569800-50571000	Enhancers	Fetal Lung	lung
47	chr7:50569800-50571000	Enhancers	Right Atrium	heart
48	chr7:50569800-50571000	Enhancers	Osteobl	bone
49	chr7:50569800-50571200	Enhancers	Fetal Muscle Trunk	muscle
50	chr7:50569800-50571200	Enhancers	Ovary	ovary

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