Variant report

Variant	rs12022525
Chromosome Location	chr1:95505324-95505325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10747462	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10874900	0.94[EUR][1000 genomes]
rs10874901	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11165285	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11165290	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11165291	0.96[EUR][1000 genomes]
rs11165292	0.93[EUR][1000 genomes]
rs11165296	0.95[EUR][1000 genomes]
rs11165301	0.87[EUR][1000 genomes]
rs12036045	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.96[TSI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12060761	0.85[EUR][1000 genomes]
rs12082888	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12120694	0.87[EUR][1000 genomes]
rs12137144	0.94[CEU][hapmap];0.82[MEX][hapmap]
rs12142814	1.00[YRI][hapmap]
rs12402604	0.98[EUR][1000 genomes]
rs12408845	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs17100482	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17112867	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4427415	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4565770	0.88[AMR][1000 genomes]
rs57001838	0.85[EUR][1000 genomes]
rs60219865	0.86[AFR][1000 genomes]
rs7526765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes]
rs7539517	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7540080	0.90[EUR][1000 genomes]
rs7551774	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3402740	chr1:95500980-95527860	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12022525	GFI1	cis	parietal	SCAN
rs12022525	C1orf146	cis	cerebellum	SCAN
rs12022525	FNBP1L	cis	cerebellum	SCAN
rs12022525	FNBP1L	cis	parietal	SCAN
rs12022525	PTBP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95480000-95508800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:95485200-95507000	Weak transcription	Fetal Heart	heart
3	chr1:95488000-95507000	Weak transcription	Ovary	ovary
4	chr1:95488200-95505400	Weak transcription	Pancreas	Pancrea
5	chr1:95488200-95507000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:95488200-95537600	Weak transcription	Right Ventricle	heart
7	chr1:95488400-95507000	Weak transcription	Brain Angular Gyrus	brain
8	chr1:95488400-95507800	Weak transcription	Brain Substantia Nigra	brain
9	chr1:95488600-95507800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:95488800-95505400	Weak transcription	Small Intestine	intestine
11	chr1:95489400-95517200	Weak transcription	Aorta	Aorta
12	chr1:95491400-95507000	Weak transcription	Fetal Kidney	kidney
13	chr1:95491600-95529600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:95492600-95507800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:95492800-95507000	Weak transcription	Fetal Stomach	stomach
16	chr1:95492800-95508800	Weak transcription	Primary T cells from cord blood	blood
17	chr1:95493400-95508800	Weak transcription	Liver	Liver
18	chr1:95495200-95508000	Weak transcription	HepG2	liver
19	chr1:95495200-95508800	Weak transcription	Fetal Intestine Small	intestine
20	chr1:95495400-95505800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:95495400-95507000	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:95497000-95508000	Weak transcription	Left Ventricle	heart
23	chr1:95500600-95507000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:95501200-95505800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:95501200-95505800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:95501200-95505800	Weak transcription	HSMMtube	muscle
27	chr1:95501400-95506800	Weak transcription	NHLF	lung
28	chr1:95501800-95506000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:95501800-95506000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:95501800-95506000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:95501800-95506800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:95501800-95507000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:95501800-95507000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:95502000-95507000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:95502000-95512200	Weak transcription	GM12878-XiMat	blood
36	chr1:95502600-95508000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:95502600-95509000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:95503200-95505800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:95504400-95506200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:95504400-95506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:95504400-95507200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:95504400-95507200	Enhancers	NHEK	skin
43	chr1:95504400-95507400	Enhancers	HMEC	breast
44	chr1:95504600-95506200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr1:95504800-95505400	Enhancers	Osteobl	bone
46	chr1:95504800-95505600	Enhancers	NH-A	brain
47	chr1:95504800-95506200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:95504800-95506800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:95505000-95507800	Enhancers	HSMM	muscle
50	chr1:95505000-95508800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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