Variant report

Variant	rs12695246
Chromosome Location	chr3:111568428-111568429
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	chr3:111566221..111568973-chr3:111577173..111579400,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10212121	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs10804493	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934114	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs10934116	0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11711475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11717092	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12490718	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs1282931	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs1282932	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1282970	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs13063024	0.93[EUR][1000 genomes]
rs13063315	0.93[EUR][1000 genomes]
rs13083516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13101043	0.93[EUR][1000 genomes]
rs1913493	0.93[EUR][1000 genomes]
rs1913494	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs3925080	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs3925081	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4381907	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4383483	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4583615	0.92[EUR][1000 genomes]
rs4610200	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6438015	0.82[JPT][hapmap]
rs6794180	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs6809414	0.86[JPT][hapmap]
rs7626131	0.92[EUR][1000 genomes]
rs7637689	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7638138	0.88[EUR][1000 genomes]
rs9288930	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs937553	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs937554	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs967011	0.93[EUR][1000 genomes]
rs9814037	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs9827362	0.85[EUR][1000 genomes]
rs9846313	0.93[EUR][1000 genomes]
rs9883806	0.96[CEU][hapmap];0.93[EUR][1000 genomes]

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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12695246	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111541200-111577600	Weak transcription	Pancreas	Pancrea
2	chr3:111563000-111577400	Weak transcription	HepG2	liver
3	chr3:111563800-111571200	Weak transcription	Stomach Mucosa	stomach
4	chr3:111565000-111571200	Enhancers	Placenta	Placenta
5	chr3:111565400-111569400	Weak transcription	NHLF	lung
6	chr3:111565600-111570200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:111565800-111570200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:111565800-111570200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:111565800-111570600	Weak transcription	HSMM	muscle
10	chr3:111566000-111569600	Weak transcription	Osteobl	bone
11	chr3:111566000-111571400	Weak transcription	Fetal Heart	heart
12	chr3:111566200-111570000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:111566200-111570000	Weak transcription	NH-A	brain
14	chr3:111566200-111570400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:111566200-111577400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:111567200-111570800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:111567600-111569000	Weak transcription	HUVEC	blood vessel
18	chr3:111567600-111570400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:111567600-111570400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:111567600-111570400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:111567800-111570200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:111567800-111570200	Weak transcription	Small Intestine	intestine
23	chr3:111567800-111570200	Weak transcription	A549	lung
24	chr3:111567800-111577400	Weak transcription	Liver	Liver
25	chr3:111567800-111577400	Weak transcription	NHDF-Ad	bronchial
26	chr3:111568000-111570000	Weak transcription	HMEC	breast
27	chr3:111568000-111570200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:111568000-111571400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:111568200-111569200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:111568200-111569400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:111568200-111569600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:111568200-111570000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:111568400-111569400	Weak transcription	Hela-S3	cervix
34	chr3:111568400-111570000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:111568400-111570000	Weak transcription	NHEK	skin
36	chr3:111568400-111570600	Weak transcription	Fetal Intestine Large	intestine

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