Variant report

Variant	rs2876273
Chromosome Location	chr6:12484118-12484119
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	chr6:12483950..12485780-chr6:12486310..12488528,2	MCF-7	breast:
2	chr6:12288090..12290509-chr6:12483279..12484840,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10807283	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190676	0.82[ASN][1000 genomes]
rs12200793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13211009	0.88[JPT][hapmap]
rs1413510	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1413511	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1999622	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999623	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2050290	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2327585	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35802624	0.92[ASN][1000 genomes]
rs7740778	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7743158	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753779	0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296391	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9296392	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9296393	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9369371	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9381187	0.94[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9381193	0.87[AMR][1000 genomes]
rs9381200	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9381210	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9381221	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9381224	0.92[ASN][1000 genomes]
rs9394914	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9394922	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9462831	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9471883	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9471890	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2876273	PAK1IP1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12471600-12484800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:12482200-12484400	Enhancers	Primary hematopoietic stem cells	blood
3	chr6:12482200-12485400	Enhancers	Fetal Intestine Small	intestine
4	chr6:12482400-12485200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:12482600-12486200	Enhancers	HMEC	breast
6	chr6:12482800-12484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:12483000-12484400	Enhancers	NHLF	lung
8	chr6:12483400-12484200	Flanking Active TSS	A549	lung
9	chr6:12483400-12484200	Flanking Active TSS	Hela-S3	cervix
10	chr6:12483400-12484200	Enhancers	HSMM	muscle
11	chr6:12483400-12484200	Flanking Active TSS	NHDF-Ad	bronchial
12	chr6:12483400-12484400	Enhancers	Aorta	Aorta
13	chr6:12483400-12484400	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:12483600-12484200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:12483600-12485400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:12483600-12485400	Enhancers	Stomach Mucosa	stomach
17	chr6:12483600-12486600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:12483800-12484200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:12483800-12484200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:12483800-12484200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:12483800-12484200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:12483800-12484200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:12483800-12484200	Active TSS	Adipose Nuclei	Adipose
24	chr6:12483800-12484200	Enhancers	Thymus	Thymus
25	chr6:12483800-12484200	Flanking Active TSS	Osteobl	bone
26	chr6:12483800-12484400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:12483800-12484400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:12483800-12484400	Active TSS	Primary B cells from cord blood	blood
29	chr6:12483800-12484400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr6:12483800-12484400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:12483800-12484400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:12483800-12484600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:12483800-12484800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:12483800-12485000	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr6:12483800-12485400	Flanking Active TSS	HUVEC	blood vessel
36	chr6:12484000-12484200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:12484000-12484200	Enhancers	Esophagus	oesophagus
38	chr6:12484000-12484200	Enhancers	Fetal Thymus	thymus
39	chr6:12484000-12484200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:12484000-12484400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:12484000-12484400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:12484000-12484400	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr6:12484000-12484400	Enhancers	Right Atrium	heart
44	chr6:12484000-12484400	Enhancers	Small Intestine	intestine
45	chr6:12484000-12484400	Enhancers	NHEK	skin
46	chr6:12484000-12484600	Enhancers	Fetal Intestine Large	intestine
47	chr6:12484000-12485400	Enhancers	NH-A	brain
48	chr6:12484000-12486400	Enhancers	HepG2	liver

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