Variant report

Variant	rs6693492
Chromosome Location	chr1:214685978-214685979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:214683964..214686596-chr1:214687813..214690608,3	MCF-7	breast:
2	chr1:214648053..214650360-chr1:214683258..214686104,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12073252	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128203	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562411	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12562873	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]
rs12563954	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565246	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17042140	0.83[CHB][hapmap]
rs28523586	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34952927	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4375231	0.81[AMR][1000 genomes]
rs4414018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59286012	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540844	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs6665807	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6665957	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6665967	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680964	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6683647	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6685189	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533482	0.89[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.86[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	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6693492	PROX1	cis	cerebellum	SCAN

Chromatin state (count:51 , 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	chr1:214671800-214686800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:214674200-214687200	Weak transcription	HSMMtube	muscle
5	chr1:214674600-214686800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:214677200-214690200	Weak transcription	Small Intestine	intestine
7	chr1:214678000-214686800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:214678200-214687800	Weak transcription	Lung	lung
9	chr1:214679000-214687400	Weak transcription	Ovary	ovary
10	chr1:214679200-214687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:214679600-214687600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:214680800-214686800	Weak transcription	HSMM	muscle
13	chr1:214680800-214687600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:214680800-214687600	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:214680800-214687800	Weak transcription	Left Ventricle	heart
16	chr1:214681000-214686600	Weak transcription	NH-A	brain
17	chr1:214681000-214687200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:214681000-214688000	Weak transcription	Hela-S3	cervix
19	chr1:214681200-214688200	Weak transcription	Fetal Kidney	kidney
20	chr1:214681400-214686800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:214681600-214690200	Weak transcription	Pancreas	Pancrea
22	chr1:214681800-214686000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:214683800-214686800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:214683800-214686800	Weak transcription	A549	lung
25	chr1:214683800-214688000	Weak transcription	Gastric	stomach
26	chr1:214684200-214686600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:214684200-214686800	Weak transcription	NHEK	skin
28	chr1:214684200-214688000	Weak transcription	HMEC	breast
29	chr1:214684400-214686000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:214684400-214686400	Weak transcription	Osteobl	bone
31	chr1:214684400-214686800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:214684600-214686000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:214684600-214687200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:214684800-214688200	Enhancers	Psoas Muscle	Psoas
35	chr1:214685200-214686000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:214685200-214686400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:214685200-214688400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:214685400-214687000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:214685400-214687600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:214685600-214686800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:214685600-214687800	Weak transcription	Fetal Stomach	stomach
42	chr1:214685600-214688200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:214685800-214686800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:214685800-214686800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:214685800-214686800	Weak transcription	HUVEC	blood vessel
46	chr1:214685800-214687000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:214685800-214687000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:214685800-214687000	Weak transcription	NHDF-Ad	bronchial
49	chr1:214685800-214687600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:214685800-214687600	Weak transcription	Fetal Muscle Leg	muscle

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