Variant report

Variant	rs4947582
Chromosome Location	chr7:50566090-50566091
allele	A/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	chr7:50565140..50566781-chr7:50570058..50572270,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10899734	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10899735	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10899736	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238138	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11575457	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11575461	0.89[ASN][1000 genomes]
rs11763807	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11763809	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11768267	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11980368	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12718527	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12718528	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12718529	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12718541	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12718558	0.83[AFR][1000 genomes]
rs12718574	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs13234331	0.89[EUR][1000 genomes]
rs13311361	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1349492	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1451371	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1451372	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1597639	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1901313	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2122822	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2167367	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2329365	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2876827	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3779082	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3779083	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3807562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807566	0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs3823674	0.84[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3887825	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4397355	0.84[AFR][1000 genomes]
rs4433100	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4436083	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4470989	0.86[AFR][1000 genomes]
rs4579483	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.93[ASN][1000 genomes]
rs4580999	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4947577	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4947581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948196	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4989851	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4992502	0.88[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6592952	0.81[ASW][hapmap];0.81[CHD][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs6953675	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs730092	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs732215	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7785224	0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs7802199	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7809477	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv516640	chr7:50565963-50568735	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4947582	FIGNL1	cis	Thyroid	GTEx
rs4947582	FIGNL1	cis	Nerve Tibial	GTEx
rs4947582	FIGNL1	cis	lung	GTEx
rs4947582	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs4947582	C7orf72	cis	parietal	SCAN
rs4947582	FIGNL1	cis	parietal	SCAN
rs4947582	FIGNL1	cis	cerebellum	SCAN
rs4947582	FIGNL1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50560600-50566200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr7:50560800-50581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:50562800-50566200	Enhancers	Primary hematopoietic stem cells	blood
5	chr7:50562800-50566200	Genic enhancers	Fetal Intestine Small	intestine
6	chr7:50563600-50566200	Enhancers	Duodenum Mucosa	Duodenum
7	chr7:50564000-50566200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:50564000-50566200	Enhancers	Ovary	ovary
9	chr7:50564200-50566200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:50564200-50566200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr7:50564400-50566200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:50564400-50566200	Enhancers	Adipose Nuclei	Adipose
13	chr7:50564400-50566200	Enhancers	Small Intestine	intestine
14	chr7:50564600-50566200	Enhancers	NHEK	skin
15	chr7:50564800-50566200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr7:50565000-50566600	Enhancers	HMEC	breast
17	chr7:50565200-50566200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:50565200-50566200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:50565200-50566200	Enhancers	K562	blood
20	chr7:50565200-50566800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:50565200-50568600	Weak transcription	Gastric	stomach
22	chr7:50565200-50569800	Weak transcription	Right Atrium	heart
23	chr7:50565200-50570000	Weak transcription	Left Ventricle	heart
24	chr7:50565200-50570200	Weak transcription	Lung	lung
25	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:50565400-50566400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr7:50565400-50568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr7:50565400-50569800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:50565400-50570000	Weak transcription	Pancreas	Pancrea
31	chr7:50565400-50570000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr7:50565400-50570000	Enhancers	Hela-S3	cervix
33	chr7:50565600-50566400	Enhancers	Fetal Muscle Leg	muscle
34	chr7:50565600-50569800	Weak transcription	Fetal Lung	lung
35	chr7:50565800-50566200	Enhancers	Psoas Muscle	Psoas
36	chr7:50565800-50566600	Enhancers	HUVEC	blood vessel
37	chr7:50565800-50569000	Strong transcription	HepG2	liver
38	chr7:50565800-50570000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:50566000-50566200	Enhancers	Colonic Mucosa	Colon
40	chr7:50566000-50566200	Enhancers	Fetal Stomach	stomach
41	chr7:50566000-50566200	Enhancers	Spleen	Spleen
42	chr7:50566000-50566400	Weak transcription	Fetal Intestine Large	intestine
43	chr7:50566000-50569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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