Variant report

Variant	rs3846662
Chromosome Location	chr5:74651084-74651085
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	chr5:74650912-74651253	K562	blood:	n/a	n/a
2	POLR2A	chr5:74649593-74651879	K562	blood:	n/a	n/a
3	POLR2A	chr5:74651063-74651302	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:74650964-74651342	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:74650987-74651388	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:74649780..74652799-chr5:74656910..74662122,4	K562	blood:
2	chr5:74632373..74634214-chr5:74651079..74652927,2	MCF-7	breast:
3	chr5:74645396..74648342-chr5:74649968..74653709,3	K562	blood:

Variant related genes	Relation type
HMGCR	TF binding region
ENSG00000113161	Chromatin interaction
ENSG00000271815	Chromatin interaction
ENSG00000247372	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10038095	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10045497	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10474433	0.86[GIH][hapmap]
rs11749783	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12654264	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17244834	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2126736	0.85[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]
rs2878417	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2878419	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3843480	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3843481	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3843482	0.88[ASN][1000 genomes]
rs3846661	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3846663	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549504	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4604177	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4704200	0.85[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap]
rs4704208	0.82[ASN][1000 genomes]
rs4704210	0.84[ASN][1000 genomes]
rs4704219	0.86[AFR][1000 genomes]
rs4704220	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4704221	0.80[AFR][1000 genomes]
rs4704223	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs5744552	0.86[AFR][1000 genomes]
rs6453131	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453133	0.85[ASN][1000 genomes]
rs6873472	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6878990	0.89[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6882842	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6896136	0.86[AFR][1000 genomes]
rs7703051	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7733436	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv882192	chr5:74641707-74707762	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Cholesterol, total	19060911	GWAS catalog
LDL cholesterol	19060911	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3846662	POC5	cis	parietal	SCAN
rs3846662	ANKRA2	cis	cerebellum	SCAN
rs3846662	HMGCR	cis	cerebellum	SCAN
rs3846662	HMGCR	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74634400-74652400	Weak transcription	Right Ventricle	heart
2	chr5:74635000-74652600	Weak transcription	Fetal Heart	heart
3	chr5:74635600-74659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:74636800-74659200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:74637200-74655800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:74637200-74659600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:74637800-74658400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:74637800-74658800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:74638200-74658400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:74638200-74659800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr5:74638200-74660400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:74638200-74660400	Strong transcription	Fetal Thymus	thymus
13	chr5:74638400-74657600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:74638400-74657800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr5:74638400-74659000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:74638400-74659000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr5:74638400-74659000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:74638400-74659200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:74638400-74659200	Strong transcription	Duodenum Mucosa	Duodenum
20	chr5:74638400-74659800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:74638600-74655000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:74638600-74659200	Strong transcription	Dnd41	blood
23	chr5:74638600-74659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:74638600-74659600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:74638600-74660200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:74638600-74660400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:74638800-74658800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:74638800-74658800	Strong transcription	NHEK	skin
29	chr5:74638800-74659800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:74639000-74656200	Strong transcription	Liver	Liver
31	chr5:74639000-74658000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr5:74639000-74658800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:74639000-74659000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:74639000-74659600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:74639400-74658800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:74639400-74659200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:74639400-74660000	Strong transcription	NHLF	lung
38	chr5:74639400-74660400	Strong transcription	HMEC	breast
39	chr5:74639600-74658000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr5:74639600-74659000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:74639600-74659000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:74639600-74659400	Strong transcription	Placenta	Placenta
43	chr5:74639800-74656000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:74639800-74657800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr5:74639800-74660000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:74640400-74659200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:74641000-74659200	Strong transcription	Fetal Intestine Large	intestine
48	chr5:74641200-74659000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:74641400-74658400	Strong transcription	Adipose Nuclei	Adipose
50	chr5:74641600-74656400	Strong transcription	Brain Germinal Matrix	brain

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