Variant report

Variant	rs2876829
Chromosome Location	chr7:50566762-50566763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50565140..50566781-chr7:50570058..50572270,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10239830	0.89[EUR][1000 genomes]
rs10249420	0.89[MEX][hapmap]
rs10267323	0.92[EUR][1000 genomes]
rs10271341	1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs10276473	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs10277662	0.92[EUR][1000 genomes]
rs11238133	0.87[LWK][hapmap];0.93[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs11238134	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs11575320	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs11575463	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11761683	0.87[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs11772714	1.00[CEU][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12671474	0.92[EUR][1000 genomes]
rs1376524	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17733244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1807066	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2060762	0.83[YRI][hapmap]
rs2060763	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2242042	0.85[EUR][1000 genomes]
rs2329371	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2876828	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28889020	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3735273	0.82[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs3735275	0.87[YRI][hapmap]
rs3779078	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs3807552	0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs3807555	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs3807556	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs3807558	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]
rs4449741	0.82[AMR][1000 genomes]
rs6950777	0.81[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs6963996	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs745042	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs745043	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7776816	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7785224	0.95[CHB][hapmap]
rs7790758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803440	0.82[CEU][hapmap]
rs7803788	0.89[MEX][hapmap]
rs880029	0.95[AFR][1000 genomes];1.00[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];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9942686	1.00[CEU][hapmap];0.92[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2876829	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2876829	FIGNL1	cis	Thyroid	GTEx
rs2876829	FIGNL1	cis	Artery Tibial	GTEx
rs2876829	FIGNL1	cis	Heart Left Ventricle	GTEx
rs2876829	FIGNL1	cis	lymphoblastoid	seeQTL
rs2876829	FIGNL1	cis	lung	GTEx
rs2876829	FIGNL1	cis	cerebellum	SCAN
rs2876829	FIGNL1	cis	multi-tissue	Pritchard
rs2876829	FIGNL1	cis	parietal	SCAN
rs2876829	FIGNL1	cis	Nerve Tibial	GTEx
rs2876829	FIGNL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:36 , 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	chr7:50565200-50566800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:50565200-50568600	Weak transcription	Gastric	stomach
5	chr7:50565200-50569800	Weak transcription	Right Atrium	heart
6	chr7:50565200-50570000	Weak transcription	Left Ventricle	heart
7	chr7:50565200-50570200	Weak transcription	Lung	lung
8	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:50565400-50568600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr7:50565400-50569800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:50565400-50570000	Weak transcription	Pancreas	Pancrea
13	chr7:50565400-50570000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:50565400-50570000	Enhancers	Hela-S3	cervix
15	chr7:50565600-50569800	Weak transcription	Fetal Lung	lung
16	chr7:50565800-50569000	Strong transcription	HepG2	liver
17	chr7:50565800-50570000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:50566000-50569400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:50566200-50566800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:50566200-50567600	Weak transcription	Fetal Stomach	stomach
21	chr7:50566200-50568400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr7:50566200-50568400	Weak transcription	Spleen	Spleen
23	chr7:50566200-50568600	Weak transcription	Psoas Muscle	Psoas
24	chr7:50566200-50569400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:50566200-50569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:50566200-50569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:50566200-50569600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:50566200-50569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:50566200-50569800	Weak transcription	Ovary	ovary
30	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
31	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
32	chr7:50566400-50567000	Weak transcription	Fetal Muscle Leg	muscle
33	chr7:50566400-50568800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:50566400-50572600	Strong transcription	Fetal Intestine Large	intestine
35	chr7:50566600-50567000	Weak transcription	HMEC	breast
36	chr7:50566600-50569800	Weak transcription	HUVEC	blood vessel

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