Variant report

Variant	rs728005
Chromosome Location	chr2:179251006-179251007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10201175	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204497	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1560870	0.93[GIH][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2114581	0.93[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276617	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366601	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4019558	0.93[GIH][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4404314	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4894017	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6757186	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs723841	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7589565	0.84[TSI][hapmap]
rs7589679	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs7605289	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs890579	0.96[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs919177	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9288019	0.88[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs728005	FKBP7	cis	parietal	SCAN
rs728005	CIR1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179201800-179253600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:179201800-179268200	Weak transcription	HSMM	muscle
3	chr2:179209200-179253000	Weak transcription	Esophagus	oesophagus
4	chr2:179210800-179257200	Weak transcription	Pancreas	Pancrea
5	chr2:179225000-179257800	Weak transcription	Lung	lung
6	chr2:179226600-179257200	Weak transcription	Gastric	stomach
7	chr2:179232000-179254200	Weak transcription	Hela-S3	cervix
8	chr2:179235600-179251600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:179237400-179252200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:179238400-179251400	Weak transcription	Fetal Intestine Large	intestine
11	chr2:179240000-179258200	Weak transcription	NHEK	skin
12	chr2:179240200-179256800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:179240800-179252000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:179240800-179253800	Weak transcription	Right Ventricle	heart
15	chr2:179241800-179262600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:179242200-179254600	Weak transcription	Ovary	ovary
17	chr2:179242200-179258600	Weak transcription	Brain Germinal Matrix	brain
18	chr2:179242400-179253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:179245800-179251400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:179246000-179256200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:179246400-179251400	Weak transcription	HUVEC	blood vessel
22	chr2:179246600-179257200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:179247000-179254600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:179247200-179253600	Strong transcription	Liver	Liver
25	chr2:179247800-179254600	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr2:179248000-179255000	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:179248200-179257200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:179248600-179254400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:179249000-179251800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:179249000-179253400	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:179249000-179254600	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:179249000-179262600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:179249000-179269000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:179249200-179251800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:179249200-179253200	Weak transcription	HMEC	breast
36	chr2:179249400-179252600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:179249400-179255000	Weak transcription	Fetal Brain Male	brain
38	chr2:179249400-179259400	Weak transcription	Left Ventricle	heart
39	chr2:179249600-179253200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:179249600-179254000	Weak transcription	Brain Anterior Caudate	brain
41	chr2:179249600-179255000	Weak transcription	Psoas Muscle	Psoas
42	chr2:179249600-179259800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:179249600-179264000	Weak transcription	Aorta	Aorta
44	chr2:179249800-179252000	Weak transcription	Fetal Brain Female	brain
45	chr2:179249800-179254800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:179250000-179252200	Enhancers	Osteobl	bone
47	chr2:179250400-179252000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:179250400-179252200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:179250400-179252400	Enhancers	Fetal Intestine Small	intestine
50	chr2:179250800-179253600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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