Variant report

Variant	rs7109250
Chromosome Location	chr11:71901670-71901671
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	chr11:71901535..71906562-chr11:71933469..71937383,8	MCF-7	breast:
2	chr11:71899258..71901849-chr11:71937862..71940065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165458	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10400327	1.00[MEX][hapmap]
rs12417459	0.82[CHB][hapmap]
rs1540087	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17162056	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17162064	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17162069	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17162131	1.00[MEX][hapmap]
rs17162133	1.00[MEX][hapmap]
rs17162138	1.00[MEX][hapmap]
rs2096784	1.00[MEX][hapmap]
rs3763796	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743684	1.00[MEX][hapmap]
rs7113391	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125189	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925545	1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7109250	PLOD2	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71892000-71906600	Weak transcription	Esophagus	oesophagus
2	chr11:71898400-71903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:71899400-71901800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:71899400-71902400	Enhancers	Fetal Lung	lung
5	chr11:71899600-71902000	Enhancers	Fetal Stomach	stomach
6	chr11:71899600-71903800	Enhancers	Fetal Muscle Leg	muscle
7	chr11:71899800-71903600	Enhancers	Fetal Muscle Trunk	muscle
8	chr11:71900000-71904000	Enhancers	Placenta	Placenta
9	chr11:71900200-71901800	Enhancers	Fetal Intestine Small	intestine
10	chr11:71900400-71903000	Enhancers	Hela-S3	cervix
11	chr11:71900600-71901800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:71900600-71901800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr11:71900600-71902000	Enhancers	Brain Germinal Matrix	brain
14	chr11:71900600-71903600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:71900600-71903600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:71900800-71902200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:71900800-71902800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:71900800-71903000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:71901000-71902000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:71901000-71902800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:71901200-71903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:71901200-71903200	Weak transcription	Lung	lung
23	chr11:71901200-71907000	Weak transcription	Pancreas	Pancrea
24	chr11:71901400-71901800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:71901400-71901800	Weak transcription	HSMM	muscle
26	chr11:71901400-71903200	Enhancers	HSMMtube	muscle
27	chr11:71901600-71903200	Weak transcription	Placenta Amnion	Placenta Amnion

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