Variant report

Variant	rs4883201
Chromosome Location	chr12:9082581-9082582
allele	A/G
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	chr12:9082312-9085096	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9080157..9083092-chr12:9098935..9102679,4	K562	blood:
2	chr12:9081265..9083698-chr12:9100850..9103403,2	MCF-7	breast:

Variant related genes	Relation type
PHC1	TF binding region
ENSG00000139187	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1000824	0.90[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs10129061	0.85[CEU][hapmap]
rs10771185	0.80[CHD][hapmap]
rs11611936	0.92[ASN][1000 genomes]
rs1805725	0.85[GIH][hapmap]
rs1805727	0.85[GIH][hapmap]
rs1805742	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1805743	0.83[ASN][1000 genomes]
rs1805744	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2159963	0.90[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs4639983	0.85[CEU][hapmap]
rs7297711	0.93[ASN][1000 genomes]
rs887782	0.88[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Cholesterol, total	24097068	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4883201	M6PR	cis	Whole Blood	GTEx
rs4883201	M6PR	cis	Artery Tibial	GTEx
rs4883201	PRB4	cis	cerebellum	SCAN
rs4883201	CD163	cis	parietal	SCAN
rs4883201	M6PR	cis	lung	GTEx
rs4883201	M6PR	cis	Skin Sun Exposed Lower leg	GTEx
rs4883201	KLRB1	cis	cerebellum	SCAN
rs4883201	CLEC9A	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9068200-9084000	Weak transcription	Esophagus	oesophagus
2	chr12:9068200-9086400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9068200-9088800	Weak transcription	Gastric	stomach
4	chr12:9068200-9091400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:9068200-9094200	Weak transcription	Colonic Mucosa	Colon
6	chr12:9068200-9094200	Weak transcription	Lung	lung
7	chr12:9068200-9094200	Weak transcription	Psoas Muscle	Psoas
8	chr12:9068200-9094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:9068200-9094200	Weak transcription	Small Intestine	intestine
10	chr12:9068200-9100000	Weak transcription	Stomach Mucosa	stomach
11	chr12:9068800-9084400	Weak transcription	Osteobl	bone
12	chr12:9068800-9086400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:9069000-9086400	Weak transcription	HepG2	liver
14	chr12:9069000-9094200	Weak transcription	NHLF	lung
15	chr12:9069400-9094000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:9069400-9094200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:9069600-9084400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:9069600-9092000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:9069800-9083600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:9069800-9083800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:9070400-9083400	Weak transcription	K562	blood
22	chr12:9070400-9092000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:9070400-9092000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:9070600-9092000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:9070600-9092600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:9070600-9092600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:9071000-9087800	Strong transcription	Fetal Brain Female	brain
28	chr12:9071000-9092000	Strong transcription	Fetal Muscle Leg	muscle
29	chr12:9071200-9088000	Strong transcription	Primary T cells from cord blood	blood
30	chr12:9071400-9084400	Strong transcription	Brain Germinal Matrix	brain
31	chr12:9071400-9099400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:9071600-9092000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr12:9071600-9092000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:9071600-9100000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:9072400-9092000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:9072400-9094200	Weak transcription	NHEK	skin
37	chr12:9072800-9091000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:9072800-9094200	Weak transcription	HSMM	muscle
39	chr12:9073800-9099800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:9074200-9093800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:9074400-9094000	Weak transcription	HUVEC	blood vessel
42	chr12:9074600-9094000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr12:9075400-9086400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:9075400-9086400	Weak transcription	Pancreas	Pancrea
45	chr12:9075400-9092000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr12:9075600-9086000	Weak transcription	NH-A	brain
47	chr12:9075600-9086400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:9075600-9087800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:9075800-9083600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:9075800-9084200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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