Variant report

Variant	rs12916
Chromosome Location	chr5:74656539-74656540
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	chr5:74656483-74656618	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:74656442-74656836	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:74655563-74656612	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:74652087-74663712	K562	blood:	n/a	n/a
5	POLR2A	chr5:74656522-74660873	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:74652490-74663640	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:74656383-74656672	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74653986..74657111-chr5:74658520..74660531,3	K562	blood:
2	chr5:74656438..74658329-chr5:74806583..74808480,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271815	TF binding region
ENSG00000113163	Chromatin interaction
ENSG00000122008	Chromatin interaction
ENSG00000271815	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10038095	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10045497	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11749783	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12654264	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17244834	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2126736	0.86[CHD][hapmap]
rs2878417	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2878419	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3843480	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3843481	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3843482	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3846661	0.84[ASN][1000 genomes]
rs3846662	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]
rs3846663	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4549504	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs4604177	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4704200	0.82[CHD][hapmap]
rs4704208	0.81[ASN][1000 genomes]
rs4704210	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4704220	0.80[ASN][1000 genomes]
rs4704223	0.80[ASN][1000 genomes]
rs6453131	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453133	0.85[ASN][1000 genomes]
rs6873472	0.80[ASN][1000 genomes]
rs6878990	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6882842	0.97[ASN][1000 genomes]
rs7703051	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7733436	0.92[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	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
2	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:5)

Disease	PMID	Source
Cholesterol, total	24097068	GWAS catalog
LDL cholesterol	20864672	GWAS catalog
LDL cholesterol	24097068	GWAS catalog
Cholesterol, total	20686565	GWAS catalog
LDL cholesterol	20686565	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12916	HMGCR	cis	parietal	SCAN
rs12916	HMGCR	cis	cerebellum	SCAN
rs12916	ANKRA2	cis	cerebellum	SCAN
rs12916	POC5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74635600-74659600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:74636800-74659200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:74637200-74659600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:74637800-74658400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:74637800-74658800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:74638200-74658400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:74638200-74659800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:74638200-74660400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:74638200-74660400	Strong transcription	Fetal Thymus	thymus
10	chr5:74638400-74657600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:74638400-74657800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr5:74638400-74659000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:74638400-74659000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr5:74638400-74659000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:74638400-74659200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:74638400-74659200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr5:74638400-74659800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr5:74638600-74659200	Strong transcription	Dnd41	blood
19	chr5:74638600-74659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:74638600-74659600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr5:74638600-74660200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:74638600-74660400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:74638800-74658800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:74638800-74658800	Strong transcription	NHEK	skin
25	chr5:74638800-74659800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:74639000-74658000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr5:74639000-74658800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:74639000-74659000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:74639000-74659600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:74639400-74658800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:74639400-74659200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:74639400-74660000	Strong transcription	NHLF	lung
33	chr5:74639400-74660400	Strong transcription	HMEC	breast
34	chr5:74639600-74658000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:74639600-74659000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr5:74639600-74659000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:74639600-74659400	Strong transcription	Placenta	Placenta
38	chr5:74639800-74657800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:74639800-74660000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:74640400-74659200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:74641000-74659200	Strong transcription	Fetal Intestine Large	intestine
42	chr5:74641200-74659000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:74641400-74658400	Strong transcription	Adipose Nuclei	Adipose
44	chr5:74641600-74657800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:74642000-74656800	Strong transcription	HepG2	liver
46	chr5:74642200-74658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr5:74643400-74657400	Strong transcription	A549	lung
48	chr5:74643600-74659400	Strong transcription	HUVEC	blood vessel
49	chr5:74644400-74659200	Strong transcription	NHDF-Ad	bronchial
50	chr5:74644800-74658600	Strong transcription	NH-A	brain

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