Variant report

Variant	rs12718574
Chromosome Location	chr7:50573848-50573849
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	chr7:50570130..50572623-chr7:50573822..50576522,2	K562	blood:
2	chr7:50518383..50520516-chr7:50572098..50575046,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10899736	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes]
rs11575423	0.93[ASN][1000 genomes]
rs11765748	0.82[CHB][hapmap]
rs12718558	0.94[ASN][1000 genomes]
rs12718572	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13234331	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1451371	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs1470750	0.80[CEU][hapmap];0.80[AMR][1000 genomes]
rs3470	0.94[ASN][1000 genomes]
rs3807562	0.89[EUR][1000 genomes]
rs3807563	0.81[EUR][1000 genomes]
rs3807566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3823674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329234	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4947577	0.83[CHB][hapmap]
rs4947581	0.89[EUR][1000 genomes]
rs4947582	0.84[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs6592952	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs732215	0.95[CEU][hapmap];0.86[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12718574	FIGNL1	cis	Artery Tibial	GTEx
rs12718574	FIGNL1	cis	Esophagus Muscularis	GTEx
rs12718574	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12718574	FIGNL1	cis	lung	GTEx
rs12718574	FIGNL1	cis	Thyroid	GTEx
rs12718574	FIGNL1	cis	Nerve Tibial	GTEx

Chromatin state (count:26 , 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	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
5	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
6	chr7:50568200-50574400	Enhancers	Fetal Muscle Leg	muscle
7	chr7:50569000-50592800	Weak transcription	HepG2	liver
8	chr7:50570800-50576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:50571000-50576000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:50571000-50580200	Weak transcription	Pancreas	Pancrea
11	chr7:50571000-50582400	Weak transcription	Right Atrium	heart
12	chr7:50571200-50576000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr7:50571800-50576200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:50572400-50574400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:50572400-50577000	Strong transcription	Duodenum Mucosa	Duodenum
16	chr7:50572600-50574600	Enhancers	Psoas Muscle	Psoas
17	chr7:50572600-50575400	Weak transcription	Fetal Intestine Large	intestine
18	chr7:50572800-50574400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:50572800-50574600	Enhancers	Fetal Thymus	thymus
20	chr7:50573000-50574800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr7:50573000-50575600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:50573000-50577000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:50573200-50574000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr7:50573200-50574400	Enhancers	Primary hematopoietic stem cells	blood
25	chr7:50573600-50574000	Enhancers	Thymus	Thymus
26	chr7:50573800-50575600	Weak transcription	Fetal Muscle Trunk	muscle

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