Variant report

Variant	rs7623691
Chromosome Location	chr3:156508710-156508711
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	chr3:156508375..156510192-chr3:156514735..156517661,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10936043	0.83[MEX][hapmap]
rs12107178	0.93[ASN][1000 genomes]
rs12492968	0.88[ASN][1000 genomes]
rs13061457	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs13068223	0.89[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1430408	0.89[AFR][1000 genomes]
rs1469536	0.82[GIH][hapmap]
rs2043108	0.86[AFR][1000 genomes]
rs2054880	0.89[CHB][hapmap]
rs343994	0.89[CHB][hapmap]
rs3851992	0.84[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs4098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680317	0.84[ASW][hapmap]
rs7638625	0.84[ASW][hapmap]
rs9818684	0.92[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9818780	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9859058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9867857	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878566	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7623691	PPM1L	cis	cerebellum	SCAN
rs7623691		cis	Lymphoblastoid	GTEx
rs7623691	LINC00886	cis	Adipose Subcutaneous	GTEx
rs7623691	SNORA5C	trans	cerebellum	SCAN
rs7623691	LINC00886	cis	Artery Tibial	GTEx
rs7623691	MUC7	trans	cerebellum	SCAN
rs7623691	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156494600-156510800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:156500200-156508800	Enhancers	HMEC	breast
3	chr3:156500400-156510800	Weak transcription	Stomach Mucosa	stomach
4	chr3:156501000-156510800	Weak transcription	Gastric	stomach
5	chr3:156502400-156510600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:156502600-156510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:156502800-156509000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:156502800-156510800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:156502800-156510800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:156502800-156528400	Weak transcription	Esophagus	oesophagus
11	chr3:156502800-156529000	Weak transcription	Liver	Liver
12	chr3:156504000-156509200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:156504200-156508800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:156504200-156516400	Weak transcription	Primary B cells from cord blood	blood
15	chr3:156505000-156510600	Weak transcription	GM12878-XiMat	blood
16	chr3:156505200-156510600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:156505200-156512400	Weak transcription	Pancreas	Pancrea
18	chr3:156506200-156509400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:156506600-156511400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:156507000-156509600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:156507000-156513600	Weak transcription	Hela-S3	cervix
22	chr3:156507200-156509000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:156507200-156509000	Weak transcription	HUVEC	blood vessel
24	chr3:156507200-156509400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:156507200-156509600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:156507200-156511400	Enhancers	NHEK	skin
27	chr3:156507400-156509600	Weak transcription	NH-A	brain
28	chr3:156507400-156509800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:156507400-156509800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:156507400-156510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:156507400-156510800	Weak transcription	NHLF	lung
32	chr3:156507600-156510600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:156508000-156509400	Weak transcription	Osteobl	bone
34	chr3:156508000-156511600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:156508200-156509600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:156508200-156510400	Weak transcription	A549	lung
37	chr3:156508400-156509600	Weak transcription	NHDF-Ad	bronchial
38	chr3:156508400-156510800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:156508400-156510800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:156508400-156512400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:156508600-156510000	Weak transcription	HSMM	muscle
42	chr3:156508600-156511400	Enhancers	K562	blood

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