Variant report

Variant	rs1146382
Chromosome Location	chr1:85918101-85918102
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85913232..85915386-chr1:85917552..85919124,2	K562	blood:
2	chr1:85917225..85920485-chr1:85926526..85929082,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001604	0.85[CEU][hapmap]
rs10489513	0.85[CEU][hapmap]
rs11161606	0.81[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs11161609	0.80[ASN][1000 genomes]
rs1146383	0.89[LWK][hapmap]
rs12044537	0.84[CEU][hapmap]
rs1240939	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233053	0.84[CEU][hapmap]
rs233072	0.89[CEU][hapmap]
rs233112	0.89[CEU][hapmap]
rs233118	0.89[CEU][hapmap]
rs233124	0.89[CEU][hapmap]
rs233130	0.89[CEU][hapmap]
rs2474123	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs530006	0.87[GIH][hapmap]
rs591917	0.91[CHB][hapmap]
rs648216	0.87[CHB][hapmap]
rs6576763	0.85[CEU][hapmap]
rs6576765	0.85[CEU][hapmap]
rs661686	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697083	0.89[JPT][hapmap]
rs7521189	0.87[GIH][hapmap]
rs7525786	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1146382	GBP2	cis	cerebellum	SCAN
rs1146382	BCL10	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:85907000-85919600	Weak transcription	Right Atrium	heart
3	chr1:85913800-85918400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:85913800-85918400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:85913800-85920400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:85914200-85924800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:85914400-85918800	Weak transcription	HepG2	liver
8	chr1:85915000-85919200	Weak transcription	HSMMtube	muscle
9	chr1:85915200-85918600	Weak transcription	Fetal Stomach	stomach
10	chr1:85915200-85918600	Weak transcription	Ovary	ovary
11	chr1:85915200-85918800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:85915200-85919600	Weak transcription	Aorta	Aorta
13	chr1:85915200-85927800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:85915400-85918800	Weak transcription	Fetal Brain Female	brain
15	chr1:85915400-85919000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:85915400-85919000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:85915400-85919200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:85915400-85919400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:85915600-85918400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:85915600-85919000	Weak transcription	NHLF	lung
21	chr1:85915600-85919200	Weak transcription	Brain Angular Gyrus	brain
22	chr1:85915600-85920200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:85915600-85925400	Weak transcription	Brain Germinal Matrix	brain
24	chr1:85915800-85920600	Weak transcription	Small Intestine	intestine
25	chr1:85916400-85919000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:85916400-85920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:85916400-85921800	Enhancers	Liver	Liver
28	chr1:85916600-85918800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:85916600-85920000	Genic enhancers	Osteobl	bone
30	chr1:85916800-85918600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:85916800-85919200	Enhancers	Brain Anterior Caudate	brain
32	chr1:85917000-85918400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:85917000-85922200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:85917000-85923000	Weak transcription	Psoas Muscle	Psoas
35	chr1:85917200-85918200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:85917200-85918600	Weak transcription	NHDF-Ad	bronchial
37	chr1:85917200-85920000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:85917400-85918400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:85917400-85918400	Weak transcription	Fetal Intestine Small	intestine
40	chr1:85917400-85918600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:85917400-85918600	Strong transcription	HSMM	muscle
42	chr1:85917400-85919000	Weak transcription	Pancreas	Pancrea
43	chr1:85917400-85919000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:85917400-85919400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:85917400-85919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:85917400-85919600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:85917400-85919600	Weak transcription	Lung	lung
48	chr1:85917400-85919600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:85917400-85920000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:85917400-85922400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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