Variant report

Variant	rs12562873
Chromosome Location	chr1:214694298-214694299
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214692777..214695349-chr1:214723508..214725233,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152104	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11120349	0.89[CEU][hapmap]
rs12073252	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12128203	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12562411	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12563954	0.96[ASN][1000 genomes]
rs12565246	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28523586	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34952927	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4414018	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59286012	0.96[ASN][1000 genomes]
rs6665807	0.96[ASN][1000 genomes]
rs6665957	0.96[ASN][1000 genomes]
rs6665967	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6680964	0.88[CEU][hapmap]
rs6683647	0.88[CEU][hapmap]
rs6685189	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693492	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7533482	0.84[MEX][hapmap];0.84[TSI][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12562873	PROX1	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214665400-214705400	Weak transcription	Right Ventricle	heart
2	chr1:214669800-214700400	Weak transcription	Aorta	Aorta
3	chr1:214686800-214694400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:214687800-214698400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:214688400-214697800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:214688400-214698400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:214688400-214706200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:214688400-214710600	Weak transcription	Spleen	Spleen
9	chr1:214689400-214694400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:214690200-214697600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:214690400-214695800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:214690600-214694600	Enhancers	NHDF-Ad	bronchial
13	chr1:214690600-214694800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:214690600-214696400	Weak transcription	Left Ventricle	heart
15	chr1:214690600-214697000	Weak transcription	Lung	lung
16	chr1:214690600-214697800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:214690600-214697800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:214690600-214697800	Weak transcription	Right Atrium	heart
19	chr1:214690600-214698400	Weak transcription	Esophagus	oesophagus
20	chr1:214690600-214705600	Weak transcription	Ovary	ovary
21	chr1:214690600-214705600	Weak transcription	Pancreas	Pancrea
22	chr1:214690800-214698200	Weak transcription	Stomach Mucosa	stomach
23	chr1:214691000-214695800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:214691200-214696200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:214691400-214705600	Weak transcription	Placenta	Placenta
26	chr1:214692000-214697000	Weak transcription	Gastric	stomach
27	chr1:214692200-214694600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:214692400-214696800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:214692400-214698400	Weak transcription	A549	lung
30	chr1:214692400-214710600	Weak transcription	HUVEC	blood vessel
31	chr1:214692800-214694800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:214692800-214697400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:214692800-214697600	Weak transcription	HSMM	muscle
34	chr1:214692800-214698200	Weak transcription	NHLF	lung
35	chr1:214693000-214696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:214693000-214697600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:214693000-214701000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:214693200-214697800	Weak transcription	NHEK	skin
39	chr1:214693600-214694600	Enhancers	Fetal Kidney	kidney
40	chr1:214693800-214694400	Genic enhancers	Osteobl	bone
41	chr1:214693800-214694600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr1:214693800-214694600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:214693800-214694600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:214693800-214694800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:214693800-214694800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr1:214693800-214694800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr1:214693800-214694800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr1:214694000-214694400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr1:214694000-214694400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:214694000-214694600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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