Variant report

Variant	rs2305462
Chromosome Location	chr2:173895285-173895286
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173895149..173898676-chr2:173907706..173911844,6	MCF-7	breast:
2	chr2:173892252..173896882-chr2:173939144..173942444,6	MCF-7	breast:
3	chr2:173892758..173895374-chr2:173911350..173913199,2	MCF-7	breast:
4	chr2:173895188..173897397-chr2:173924507..173926059,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12987382	0.82[JPT][hapmap]
rs3754750	0.87[GIH][hapmap];0.88[JPT][hapmap]
rs3754751	0.88[JPT][hapmap]
rs3769220	0.82[JPT][hapmap]
rs3769222	0.88[JPT][hapmap]
rs3820839	0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs729486	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2305462	ZAK	cis	cerebellum	SCAN
rs2305462	PPIG	cis	parietal	SCAN
rs2305462	GPR155	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173868000-173902000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:173877200-173901600	Weak transcription	Gastric	stomach
3	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:173881400-173897200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:173888800-173905600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:173888800-173906600	Weak transcription	Lung	lung
7	chr2:173891000-173896200	Weak transcription	Placenta	Placenta
8	chr2:173891000-173908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:173891400-173896400	Enhancers	Fetal Heart	heart
10	chr2:173892600-173897200	Enhancers	Fetal Muscle Leg	muscle
11	chr2:173892600-173897400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr2:173892600-173906800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:173892800-173895400	Weak transcription	NHEK	skin
14	chr2:173892800-173901600	Weak transcription	Pancreas	Pancrea
15	chr2:173892800-173902400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:173893000-173898600	Weak transcription	A549	lung
17	chr2:173893000-173900600	Weak transcription	Brain Angular Gyrus	brain
18	chr2:173893000-173908800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:173893000-173913200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:173893200-173898200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:173893200-173901600	Weak transcription	Right Atrium	heart
22	chr2:173893200-173902400	Weak transcription	Aorta	Aorta
23	chr2:173893200-173902600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:173893200-173922000	Weak transcription	Brain Anterior Caudate	brain
25	chr2:173893600-173896800	Strong transcription	Liver	Liver
26	chr2:173893800-173908200	Weak transcription	Right Ventricle	heart
27	chr2:173894000-173897400	Weak transcription	NHDF-Ad	bronchial
28	chr2:173894000-173897600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:173894000-173897600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:173894000-173898400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:173894000-173898800	Weak transcription	Psoas Muscle	Psoas
32	chr2:173894000-173901600	Weak transcription	Ovary	ovary
33	chr2:173894000-173902000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:173894000-173909200	Weak transcription	Fetal Stomach	stomach
35	chr2:173894400-173895800	Enhancers	Fetal Kidney	kidney
36	chr2:173894400-173900600	Weak transcription	Fetal Intestine Small	intestine
37	chr2:173894800-173895800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:173894800-173896800	Enhancers	Left Ventricle	heart
39	chr2:173895000-173895400	Enhancers	Fetal Thymus	thymus
40	chr2:173895000-173897000	Enhancers	HMEC	breast
41	chr2:173895200-173897000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:173895200-173897800	Enhancers	Skeletal Muscle Male	skeletal muscle

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