Variant report

Variant	rs2605401
Chromosome Location	chr12:42609207-42609208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42528143..42530319-chr12:42607718..42609289,2	MCF-7	breast:
2	chr12:42609074..42611841-chr12:42630116..42632105,3	MCF-7	breast:
3	chr12:42537474..42540100-chr12:42609019..42612283,3	K562	blood:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000151233	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1069644	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10785335	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10785337	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880275	0.86[CEU][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10880279	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1118483	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1226298	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1238290	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1683195	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1826387	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1961953	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2061191	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2061192	0.82[AMR][1000 genomes]
rs2085314	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2100547	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2198763	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4402364	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4417370	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768398	0.82[CEU][hapmap]
rs6582385	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6582386	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582389	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582392	0.86[CEU][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs712108	0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712109	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712112	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs712114	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712115	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712118	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs712119	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs712122	1.00[CEU][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712123	1.00[CEU][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712125	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs712126	1.00[CEU][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712129	0.84[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7298965	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7302687	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7316575	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7486516	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7956016	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7959339	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7960176	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7970115	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7975518	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs824739	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs824741	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs824742	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs866091	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv973057	chr12:42607675-42611336	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2605401	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42547800-42610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:42550600-42615800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:42552200-42613000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:42552400-42620000	Weak transcription	Fetal Brain Female	brain
5	chr12:42555000-42628600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:42556800-42613200	Weak transcription	HMEC	breast
7	chr12:42568400-42623400	Weak transcription	K562	blood
8	chr12:42568800-42630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:42569600-42630800	Weak transcription	Colonic Mucosa	Colon
10	chr12:42569800-42631000	Weak transcription	Gastric	stomach
11	chr12:42574800-42615600	Weak transcription	HUVEC	blood vessel
12	chr12:42575600-42628600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:42586800-42630000	Weak transcription	Fetal Kidney	kidney
14	chr12:42587200-42629600	Weak transcription	Lung	lung
15	chr12:42587400-42620000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:42587800-42619400	Weak transcription	Fetal Lung	lung
17	chr12:42587800-42623400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:42588400-42628600	Weak transcription	Thymus	Thymus
19	chr12:42590200-42610400	Weak transcription	HSMMtube	muscle
20	chr12:42591600-42628200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:42593000-42613000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:42593200-42620000	Weak transcription	Dnd41	blood
23	chr12:42594000-42615400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:42594400-42615400	Weak transcription	Primary T cells from cord blood	blood
25	chr12:42595200-42611800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:42600400-42610600	Weak transcription	NHLF	lung
27	chr12:42600600-42611600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:42602400-42628600	Weak transcription	Spleen	Spleen
29	chr12:42602400-42630800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:42602800-42611800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:42602800-42613200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:42602800-42628800	Weak transcription	HepG2	liver
33	chr12:42603000-42620200	Weak transcription	Primary B cells from cord blood	blood
34	chr12:42603600-42625800	Weak transcription	GM12878-XiMat	blood
35	chr12:42604400-42610600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:42604400-42611200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:42604400-42611600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:42604400-42618800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:42604400-42619400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:42604400-42620000	Weak transcription	Liver	Liver
41	chr12:42604400-42623400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:42604400-42627400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:42604400-42628000	Weak transcription	Placenta	Placenta
44	chr12:42604600-42610400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:42604600-42611400	Weak transcription	NH-A	brain
46	chr12:42604600-42611600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:42604600-42611600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:42604600-42611600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:42604600-42611600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr12:42604600-42611800	Weak transcription	Primary monocytes fromperipheralblood	blood

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