Variant report

Variant	rs3747562
Chromosome Location	chr12:42854205-42854206
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	chr12:42853924..42855484-chr12:42857637..42859373,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10880284	0.81[CEU][hapmap]
rs11832772	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423383	0.81[CEU][hapmap]
rs12425945	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs12578312	0.81[CEU][hapmap]
rs1376931	0.81[CEU][hapmap]
rs1669884	0.81[CEU][hapmap]
rs1669903	0.81[CEU][hapmap]
rs1669937	0.81[CEU][hapmap]
rs1796357	0.81[CEU][hapmap]
rs1796389	0.81[CEU][hapmap]
rs1796398	0.81[CEU][hapmap]
rs2243465	0.81[CEU][hapmap]
rs3761677	0.81[CEU][hapmap]
rs3827524	0.81[CEU][hapmap]
rs4768401	0.81[CEU][hapmap]
rs7134130	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896555	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3747562	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42816200-42858200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:42820000-42858200	Weak transcription	Gastric	stomach
4	chr12:42826400-42859000	Weak transcription	Fetal Brain Male	brain
5	chr12:42826600-42858200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
7	chr12:42834200-42859600	Weak transcription	Brain Substantia Nigra	brain
8	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
9	chr12:42836800-42858800	Weak transcription	Brain Angular Gyrus	brain
10	chr12:42837000-42858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:42837000-42858000	Weak transcription	Aorta	Aorta
12	chr12:42837000-42858200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
14	chr12:42837200-42863200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:42838400-42858000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:42840000-42856400	Weak transcription	Fetal Intestine Small	intestine
17	chr12:42840400-42860800	Weak transcription	Colonic Mucosa	Colon
18	chr12:42840600-42858000	Weak transcription	Placenta	Placenta
19	chr12:42840600-42860000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:42840800-42858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:42841000-42858600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:42841400-42856400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:42841400-42862000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:42841600-42858400	Weak transcription	Fetal Brain Female	brain
25	chr12:42841600-42862400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:42843000-42862400	Weak transcription	Fetal Thymus	thymus
27	chr12:42843200-42858200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:42843200-42858200	Weak transcription	Pancreas	Pancrea
29	chr12:42843200-42862000	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:42843600-42862400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:42844000-42856400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:42844400-42858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:42844800-42862600	Weak transcription	Primary T cells from cord blood	blood
34	chr12:42845000-42857600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:42845200-42856400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:42849400-42864800	Strong transcription	Fetal Stomach	stomach
37	chr12:42850000-42860800	Strong transcription	HSMMtube	muscle
38	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:42850200-42855000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:42850200-42859800	Strong transcription	Primary B cells from cord blood	blood
41	chr12:42850200-42860600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:42850200-42862800	Strong transcription	NH-A	brain
43	chr12:42850200-42865000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:42850200-42865000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr12:42850200-42865800	Strong transcription	Osteobl	bone
46	chr12:42850800-42860400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:42851400-42860800	Strong transcription	HSMM	muscle
48	chr12:42851600-42854600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:42851800-42855400	Strong transcription	HMEC	breast
50	chr12:42851800-42863000	Strong transcription	Fetal Muscle Leg	muscle

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