Variant report

Variant	rs11750407
Chromosome Location	chr5:178353321-178353322
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10516151	0.82[GIH][hapmap]
rs11249605	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016198	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34797550	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4700746	0.80[CHB][hapmap]
rs4700972	0.80[CHB][hapmap]
rs7701540	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7702879	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv821324	chr5:178345876-178353585	ZNF genes & repeats Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv5156	chr5:178346825-178367067	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv1835389	chr5:178348445-178353321	Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1837400	chr5:178348445-178353321	ZNF genes & repeats Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1839542	chr5:178348445-178353321	ZNF genes & repeats Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1841499	chr5:178348554-178353321	ZNF genes & repeats Weak transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv964988	chr5:178349100-178353458	ZNF genes & repeats Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11750407	N4BP3	cis	parietal	SCAN
rs11750407	HNRNPAB	cis	parietal	SCAN
rs11750407	GFPT2	cis	parietal	SCAN
rs11750407	ZNF454	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr5:178341600-178367000	ZNF genes & repeats	Fetal Brain Female	brain
3	chr5:178343000-178367200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr5:178347800-178366800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
5	chr5:178347800-178367400	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr5:178348000-178359800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:178348000-178360200	ZNF genes & repeats	Left Ventricle	heart
8	chr5:178348800-178357800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:178351400-178367400	ZNF genes & repeats	Brain Anterior Caudate	brain
10	chr5:178351600-178359600	ZNF genes & repeats	Aorta	Aorta
11	chr5:178352200-178359200	ZNF genes & repeats	Brain Germinal Matrix	brain
12	chr5:178352200-178363200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
13	chr5:178352200-178366800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
14	chr5:178352200-178367200	ZNF genes & repeats	Brain Substantia Nigra	brain
15	chr5:178352400-178354400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:178352400-178360200	ZNF genes & repeats	Ovary	ovary
17	chr5:178352400-178369200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:178352600-178353800	Weak transcription	Brain Angular Gyrus	brain
19	chr5:178352600-178353800	Weak transcription	Pancreas	Pancrea
20	chr5:178352600-178357000	Weak transcription	Fetal Heart	heart
21	chr5:178352800-178353600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:178352800-178353800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:178352800-178354200	ZNF genes & repeats	Fetal Intestine Large	intestine

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