Variant report

Variant	rs7960176
Chromosome Location	chr12:42629550-42629551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:42629535-42629735	MCF10A-Er-Src	breast:	n/a	n/a
2	NR3C1	chr12:42629200-42629622	A549	lung:	n/a	chr12:42629419-42629437 chr12:42629420-42629436 chr12:42629417-42629438 chr12:42629420-42629436 chr12:42629421-42629435 chr12:42629415-42629441 chr12:42629420-42629436 chr12:42629420-42629436 chr12:42629421-42629435 chr12:42629418-42629439 chr12:42629232-42629258
3	NR3C1	chr12:42629274-42629572	A549	lung:	n/a	chr12:42629419-42629437 chr12:42629420-42629436 chr12:42629417-42629438 chr12:42629420-42629436 chr12:42629421-42629435 chr12:42629415-42629441 chr12:42629420-42629436 chr12:42629420-42629436 chr12:42629421-42629435 chr12:42629418-42629439

No.	Distal block	Cell Line	Cell type
1	chr12:42629382..42633215-chr12:42724719..42729481,4	MCF-7	breast:
2	chr12:42625009..42627071-chr12:42627822..42629813,2	MCF-7	breast:
3	chr12:42602650..42606559-chr12:42628357..42633249,5	MCF-7	breast:
4	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
5	chr12:42613730..42615825-chr12:42628835..42630747,2	K562	blood:

Variant related genes	Relation type
PPHLN1	TF binding region
ENSG00000134283	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000015153	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1069644	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785335	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785337	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880280	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880284	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs11181461	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs1118483	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226298	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1226303	0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs1238290	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423383	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs12425945	0.92[CEU][hapmap]
rs12578312	0.92[CEU][hapmap]
rs1376931	0.82[ASW][hapmap];0.92[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs1463613	0.93[JPT][hapmap]
rs1628871	0.92[JPT][hapmap]
rs1669903	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1669937	0.92[CEU][hapmap]
rs1683195	0.88[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17091052	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732351	0.82[GIH][hapmap];0.87[JPT][hapmap]
rs1732352	0.87[JPT][hapmap]
rs1796357	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs1796389	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1796398	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs1826387	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961953	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2061191	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2061192	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085314	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2100547	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2198763	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243465	0.82[ASW][hapmap];0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs2605401	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3761677	0.92[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap]
rs3827524	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs4402364	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417370	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768397	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs4768398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs4768401	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs6582378	0.83[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap]
rs6582385	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582386	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6582389	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712106	0.93[JPT][hapmap]
rs712108	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712109	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs712112	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712114	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712115	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712118	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712119	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs712120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712122	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712123	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712125	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712126	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs712127	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs712129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134895	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7298965	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302687	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303028	0.83[GIH][hapmap]
rs7316575	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7486516	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7956016	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7959339	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975518	0.88[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7978993	0.87[JPT][hapmap]
rs824716	0.87[JPT][hapmap]
rs824724	0.87[JPT][hapmap]
rs824734	0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs824738	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs824739	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs824741	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs824742	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs844046	0.93[JPT][hapmap]
rs865420	0.88[CHD][hapmap];0.93[JPT][hapmap]
rs866091	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7960176	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42568800-42630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:42569600-42630800	Weak transcription	Colonic Mucosa	Colon
3	chr12:42569800-42631000	Weak transcription	Gastric	stomach
4	chr12:42586800-42630000	Weak transcription	Fetal Kidney	kidney
5	chr12:42587200-42629600	Weak transcription	Lung	lung
6	chr12:42602400-42630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:42607800-42630600	Weak transcription	NHEK	skin
8	chr12:42608200-42630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:42609800-42631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:42613600-42631000	Weak transcription	Ovary	ovary
11	chr12:42613800-42630800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:42616400-42629600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:42620400-42630800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:42620400-42631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:42620600-42630000	Weak transcription	HMEC	breast
16	chr12:42620600-42630200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:42620600-42630800	Weak transcription	Fetal Intestine Small	intestine
18	chr12:42620600-42630800	Weak transcription	Fetal Stomach	stomach
19	chr12:42623400-42629600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:42625200-42629600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:42625800-42629600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:42626400-42629600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:42627200-42630800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:42627400-42629600	Strong transcription	Fetal Intestine Large	intestine
25	chr12:42627800-42629600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:42627800-42629600	Weak transcription	Left Ventricle	heart
27	chr12:42627800-42629800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:42628000-42629600	Strong transcription	Placenta	Placenta
29	chr12:42628000-42631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:42628200-42629600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:42628200-42629600	Genic enhancers	Dnd41	blood
32	chr12:42628200-42629600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
33	chr12:42628200-42630600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:42628200-42631000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:42628400-42630600	Enhancers	Liver	Liver
36	chr12:42628600-42629600	Genic enhancers	Primary T cells from cord blood	blood
37	chr12:42628600-42629600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr12:42628600-42629600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:42628600-42629800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:42628600-42629800	Enhancers	Pancreas	Pancrea
41	chr12:42628600-42629800	Enhancers	Psoas Muscle	Psoas
42	chr12:42628600-42629800	Enhancers	Spleen	Spleen
43	chr12:42628600-42630000	Enhancers	Adipose Nuclei	Adipose
44	chr12:42628600-42630000	Enhancers	Brain Angular Gyrus	brain
45	chr12:42628600-42630000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr12:42628600-42630000	Enhancers	NHDF-Ad	bronchial
47	chr12:42628600-42630400	Enhancers	Brain Cingulate Gyrus	brain
48	chr12:42628600-42630800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr12:42628600-42630800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr12:42628600-42630800	Enhancers	Brain Substantia Nigra	brain

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