Variant report

Variant	rs4045166
Chromosome Location	chr5:74909446-74909447
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74905446..74908420-chr5:74909324..74911813,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189045	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10043621	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10044053	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10060260	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10067641	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10075139	0.82[EUR][1000 genomes]
rs10434644	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10474436	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1051795	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10942739	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11957913	0.85[EUR][1000 genomes]
rs13354407	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1427924	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17739580	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1863934	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1863935	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1995267	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2287711	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs253392	0.81[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs253393	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs253407	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs253408	0.86[ASN][1000 genomes]
rs253409	0.95[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs28609217	0.87[EUR][1000 genomes]
rs2878519	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2878520	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213801	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34340	0.92[ASN][1000 genomes]
rs34344	0.84[ASN][1000 genomes]
rs34345	0.84[ASN][1000 genomes]
rs3761743	0.85[EUR][1000 genomes]
rs3846666	0.87[EUR][1000 genomes]
rs4385188	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4440336	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4703674	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704224	0.93[EUR][1000 genomes]
rs4704228	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57149337	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57312935	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744533	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744555	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5744575	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744595	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5744598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744601	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744621	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5744663	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5744703	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59506842	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61430233	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453134	0.90[EUR][1000 genomes]
rs67969809	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6861279	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6863398	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6872314	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6874781	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6886841	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6891949	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73120833	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7445415	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs767676	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7706857	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7709282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7717505	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7723531	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924452	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9293656	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9332464	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4045166	S100Z	cis	parietal	SCAN
rs4045166	COL4A3BP	cis	cerebellum	SCAN
rs4045166	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74907400-74909800	Weak transcription	K562	blood
2	chr5:74907800-74912200	Weak transcription	HSMMtube	muscle
3	chr5:74907800-74913000	Weak transcription	Fetal Brain Male	brain
4	chr5:74907800-74921400	Weak transcription	Aorta	Aorta
5	chr5:74907800-74921400	Weak transcription	Lung	lung
6	chr5:74908000-74910000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:74908000-74911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:74908000-74912000	Weak transcription	Stomach Mucosa	stomach
9	chr5:74908000-74912600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:74908000-74912800	Weak transcription	Placenta	Placenta
11	chr5:74908000-74912800	Weak transcription	HMEC	breast
12	chr5:74908000-74913600	Weak transcription	Colonic Mucosa	Colon
13	chr5:74908000-74916000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:74908200-74911600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:74908200-74912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:74908200-74912600	Weak transcription	Fetal Brain Female	brain
17	chr5:74908200-74918800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:74908200-74919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:74908200-74923600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:74908400-74911200	Weak transcription	Fetal Stomach	stomach
21	chr5:74908400-74911600	Weak transcription	Fetal Kidney	kidney
22	chr5:74908400-74912200	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:74908400-74912200	Weak transcription	NH-A	brain
24	chr5:74908400-74912400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:74908400-74912600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:74908400-74912600	Weak transcription	HSMM	muscle
27	chr5:74908400-74913000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:74908400-74913200	Weak transcription	Osteobl	bone
29	chr5:74908400-74913600	Weak transcription	Gastric	stomach
30	chr5:74908600-74910000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:74908600-74911800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr5:74908600-74912200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:74908600-74913400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:74908600-74918000	Weak transcription	Small Intestine	intestine
35	chr5:74908600-74920400	Enhancers	Fetal Intestine Small	intestine
36	chr5:74908800-74912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:74909000-74909600	Enhancers	Fetal Lung	lung
38	chr5:74909000-74909800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr5:74909000-74911400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:74909000-74912400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:74909000-74912800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:74909000-74916000	Weak transcription	A549	lung
43	chr5:74909200-74912200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:74909400-74910400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr5:74909400-74911400	Enhancers	Fetal Intestine Large	intestine

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