Variant report

Variant	rs7975518
Chromosome Location	chr12:42617901-42617902
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42617053..42619651-chr12:42629734..42632982,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1064469	0.87[MEX][hapmap]
rs1069644	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10785335	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10785337	0.81[EUR][1000 genomes]
rs10880275	0.88[CEU][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880279	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10880284	0.80[CEU][hapmap]
rs1118483	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1226298	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1226303	0.91[MEX][hapmap]
rs1238290	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12423383	0.80[CEU][hapmap]
rs12425945	0.86[CHB][hapmap]
rs12578312	0.80[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1376931	0.80[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs1669903	0.80[CEU][hapmap]
rs1669937	0.81[CHB][hapmap]
rs1683195	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1732351	0.83[MEX][hapmap]
rs1796357	0.80[CEU][hapmap]
rs1826387	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1961953	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2061191	0.81[EUR][1000 genomes]
rs2085314	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2100547	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2198763	0.85[EUR][1000 genomes]
rs2243465	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap]
rs2605401	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3761677	0.80[CEU][hapmap]
rs3827524	0.80[CEU][hapmap]
rs3990966	0.83[MEX][hapmap]
rs4402364	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4417370	0.89[EUR][1000 genomes]
rs4768398	0.84[CEU][hapmap]
rs4768401	0.80[CEU][hapmap]
rs6582378	0.91[MEX][hapmap]
rs6582383	0.83[MEX][hapmap]
rs6582385	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6582386	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6582389	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582392	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs712108	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712109	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712112	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs712114	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712115	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712118	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712119	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs712122	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712123	1.00[CEU][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712125	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712127	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712129	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7134895	0.86[CEU][hapmap]
rs7135851	0.83[MEX][hapmap]
rs7297464	0.83[MEX][hapmap]
rs7298965	0.81[EUR][1000 genomes]
rs7302687	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303028	0.87[MEX][hapmap]
rs7316575	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7486516	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7956016	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7959339	0.85[EUR][1000 genomes]
rs7959852	0.83[MEX][hapmap]
rs7960176	0.88[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7964383	0.83[MEX][hapmap]
rs7970115	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7971943	0.83[MEX][hapmap]
rs824734	0.87[MEX][hapmap]
rs824739	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs824741	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs824742	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs865420	0.91[MEX][hapmap]
rs866091	0.88[AMR][1000 genomes];0.96[EUR][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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv826351	chr12:42584218-42676281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv826352	chr12:42593124-42675255	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7975518	PPHLN1	cis	multi-tissue	Pritchard
rs7975518	PPHLN1	cis	Artery Tibial	GTEx
rs7975518	MADP-1	cis	multi-tissue	Pritchard

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
2	chr12:42555000-42628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:42568400-42623400	Weak transcription	K562	blood
4	chr12:42568800-42630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:42569600-42630800	Weak transcription	Colonic Mucosa	Colon
6	chr12:42569800-42631000	Weak transcription	Gastric	stomach
7	chr12:42575600-42628600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:42586800-42630000	Weak transcription	Fetal Kidney	kidney
9	chr12:42587200-42629600	Weak transcription	Lung	lung
10	chr12:42587400-42620000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:42587800-42619400	Weak transcription	Fetal Lung	lung
12	chr12:42587800-42623400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:42588400-42628600	Weak transcription	Thymus	Thymus
14	chr12:42591600-42628200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:42593200-42620000	Weak transcription	Dnd41	blood
16	chr12:42602400-42628600	Weak transcription	Spleen	Spleen
17	chr12:42602400-42630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:42602800-42628800	Weak transcription	HepG2	liver
19	chr12:42603000-42620200	Weak transcription	Primary B cells from cord blood	blood
20	chr12:42603600-42625800	Weak transcription	GM12878-XiMat	blood
21	chr12:42604400-42618800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:42604400-42619400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:42604400-42620000	Weak transcription	Liver	Liver
24	chr12:42604400-42623400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:42604400-42627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:42604400-42628000	Weak transcription	Placenta	Placenta
27	chr12:42604600-42620000	Weak transcription	Brain Germinal Matrix	brain
28	chr12:42604600-42624400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:42604600-42626800	Weak transcription	Hela-S3	cervix
30	chr12:42604600-42628800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:42604600-42629000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:42607200-42620000	Weak transcription	Fetal Thymus	thymus
33	chr12:42607800-42630600	Weak transcription	NHEK	skin
34	chr12:42608000-42627400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:42608200-42619400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:42608200-42620200	Weak transcription	Fetal Intestine Small	intestine
37	chr12:42608200-42624200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:42608200-42628600	Weak transcription	Brain Anterior Caudate	brain
39	chr12:42608200-42630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:42608400-42628600	Weak transcription	Brain Angular Gyrus	brain
41	chr12:42608400-42628600	Weak transcription	Pancreas	Pancrea
42	chr12:42608400-42629000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:42609200-42619400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:42609200-42620000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:42609800-42631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:42612000-42628600	Weak transcription	Adipose Nuclei	Adipose
47	chr12:42612200-42619800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr12:42612200-42620000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:42612200-42623400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:42612200-42628600	Weak transcription	NHDF-Ad	bronchial

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