Variant report

Variant	rs904743
Chromosome Location	chr5:74917862-74917863
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74915137..74918881-chr5:74947780..74950531,3	K562	blood:
2	chr5:74913060..74915078-chr5:74915803..74919443,3	K562	blood:
3	chr5:74910178..74911723-chr5:74917267..74920194,2	K562	blood:
4	chr5:74912858..74914560-chr5:74917246..74919606,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10036682	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10038945	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10041470	0.89[EUR][1000 genomes]
rs10055011	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10059022	1.00[ASW][hapmap];0.93[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10061689	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10067900	0.85[EUR][1000 genomes]
rs10074747	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10076819	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10077427	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10078671	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10474437	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12173076	0.81[EUR][1000 genomes]
rs13360099	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13361353	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469051	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1553234	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1820049	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1909719	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287710	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs253410	0.84[ASN][1000 genomes]
rs28408106	0.85[EUR][1000 genomes]
rs28612248	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28668361	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28874007	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34339	0.84[ASN][1000 genomes]
rs34342	0.84[ASN][1000 genomes]
rs34343	0.84[ASN][1000 genomes]
rs34355	0.81[CHD][hapmap]
rs34357	0.81[CHD][hapmap]
rs3804231	0.85[EUR][1000 genomes]
rs4703675	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704229	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56859362	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5744544	0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5744545	0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5744636	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744667	0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744704	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5744709	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5744712	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57907925	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58841453	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6891560	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72633965	0.85[EUR][1000 genomes]
rs72633967	0.87[EUR][1000 genomes]
rs72633968	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72633969	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72633970	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72633971	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72633972	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633973	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633974	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72633975	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72633976	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72633977	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7726478	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9293652	0.85[EUR][1000 genomes]
rs9293654	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9293655	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs979182	0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
5	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs904743	HMGCR	cis	cerebellum	SCAN
rs904743	ARSB	cis	parietal	SCAN
rs904743	GCNT4	cis	cerebellum	SCAN
rs904743	ANKRA2	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74907800-74921400	Weak transcription	Aorta	Aorta
2	chr5:74907800-74921400	Weak transcription	Lung	lung
3	chr5:74908200-74918800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr5:74908200-74919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:74908200-74923600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:74908600-74918000	Weak transcription	Small Intestine	intestine
7	chr5:74908600-74920400	Enhancers	Fetal Intestine Small	intestine
8	chr5:74913600-74918400	Weak transcription	HSMM	muscle
9	chr5:74913800-74918200	Weak transcription	Colonic Mucosa	Colon
10	chr5:74913800-74919800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:74913800-74921400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:74913800-74921600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:74913800-74922400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:74913800-74922800	Weak transcription	Ovary	ovary
15	chr5:74913800-74923600	Weak transcription	Esophagus	oesophagus
16	chr5:74913800-74923600	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:74913800-74933600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:74914000-74918200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:74914000-74918200	Weak transcription	NH-A	brain
20	chr5:74914000-74919400	Weak transcription	HSMMtube	muscle
21	chr5:74914000-74919800	Weak transcription	Fetal Stomach	stomach
22	chr5:74914000-74923400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:74914000-74930800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:74914200-74919400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:74915000-74925800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:74915600-74918400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:74915600-74921800	Enhancers	Stomach Mucosa	stomach
28	chr5:74915800-74920000	Enhancers	Duodenum Mucosa	Duodenum
29	chr5:74916600-74931800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:74916800-74918400	Weak transcription	A549	lung
31	chr5:74916800-74919600	Weak transcription	K562	blood
32	chr5:74917000-74918000	Weak transcription	Pancreas	Pancrea
33	chr5:74917000-74918000	Weak transcription	NHEK	skin
34	chr5:74917000-74919800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:74917000-74920000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:74917000-74923400	Weak transcription	Gastric	stomach
37	chr5:74917600-74920200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:74917800-74918400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr5:74917800-74918800	Enhancers	Liver	Liver
40	chr5:74917800-74918800	Enhancers	HepG2	liver
41	chr5:74917800-74920000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:74917800-74920000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:74917800-74920200	Enhancers	HMEC	breast
44	chr5:74917800-74920400	Enhancers	Fetal Intestine Large	intestine

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