Variant report

Variant	rs1820049
Chromosome Location	chr5:74908446-74908447
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	chr5:74806025..74808781-chr5:74906137..74908952,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113163	Chromatin interaction
ENSG00000122008	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10036682	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10038945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10041470	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10055011	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10059022	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10061689	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10067900	0.88[EUR][1000 genomes]
rs10074747	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10076819	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10077427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10078671	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474437	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12173076	0.84[EUR][1000 genomes]
rs13360099	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13361353	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1469051	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1553234	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1909719	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287710	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253410	0.85[ASN][1000 genomes]
rs28408106	0.88[EUR][1000 genomes]
rs28612248	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28668361	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28874007	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34339	0.85[ASN][1000 genomes]
rs34342	0.85[ASN][1000 genomes]
rs34343	0.85[ASN][1000 genomes]
rs34349	0.80[ASN][1000 genomes]
rs3804231	0.88[EUR][1000 genomes]
rs4703675	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704229	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56859362	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5744544	0.89[EUR][1000 genomes]
rs5744545	0.88[EUR][1000 genomes]
rs5744636	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5744667	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744704	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5744709	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744712	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57907925	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58841453	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891560	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633965	0.88[EUR][1000 genomes]
rs72633966	0.81[EUR][1000 genomes]
rs72633967	0.90[EUR][1000 genomes]
rs72633968	0.87[EUR][1000 genomes]
rs72633969	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633970	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633971	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72633972	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72633973	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72633974	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72633975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633976	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633977	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7726478	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs904743	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293652	0.88[EUR][1000 genomes]
rs9293654	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9293655	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs979182	0.91[EUR][1000 genomes];0.87[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74906800-74908600	Active TSS	Fetal Intestine Small	intestine
2	chr5:74906800-74909000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr5:74907200-74908600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr5:74907400-74909800	Weak transcription	K562	blood
5	chr5:74907800-74909000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr5:74907800-74912200	Weak transcription	HSMMtube	muscle
7	chr5:74907800-74913000	Weak transcription	Fetal Brain Male	brain
8	chr5:74907800-74921400	Weak transcription	Aorta	Aorta
9	chr5:74907800-74921400	Weak transcription	Lung	lung
10	chr5:74908000-74908600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:74908000-74909000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:74908000-74909000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:74908000-74909200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:74908000-74909400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr5:74908000-74910000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:74908000-74911800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:74908000-74912000	Weak transcription	Stomach Mucosa	stomach
18	chr5:74908000-74912600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:74908000-74912800	Weak transcription	Placenta	Placenta
20	chr5:74908000-74912800	Weak transcription	HMEC	breast
21	chr5:74908000-74913600	Weak transcription	Colonic Mucosa	Colon
22	chr5:74908000-74916000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:74908200-74908600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:74908200-74908600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr5:74908200-74908600	Enhancers	Brain Anterior Caudate	brain
26	chr5:74908200-74908600	Enhancers	NHEK	skin
27	chr5:74908200-74908800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:74908200-74908800	Flanking Active TSS	Fetal Lung	lung
29	chr5:74908200-74908800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:74908200-74909000	Enhancers	A549	lung
31	chr5:74908200-74911600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:74908200-74912600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:74908200-74912600	Weak transcription	Fetal Brain Female	brain
34	chr5:74908200-74918800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:74908200-74919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:74908200-74923600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr5:74908400-74908600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:74908400-74908600	Enhancers	Duodenum Mucosa	Duodenum
39	chr5:74908400-74908600	Enhancers	Small Intestine	intestine
40	chr5:74908400-74909400	Weak transcription	Fetal Intestine Large	intestine
41	chr5:74908400-74911200	Weak transcription	Fetal Stomach	stomach
42	chr5:74908400-74911600	Weak transcription	Fetal Kidney	kidney
43	chr5:74908400-74912200	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:74908400-74912200	Weak transcription	NH-A	brain
45	chr5:74908400-74912400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:74908400-74912600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:74908400-74912600	Weak transcription	HSMM	muscle
48	chr5:74908400-74913000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:74908400-74913200	Weak transcription	Osteobl	bone
50	chr5:74908400-74913600	Weak transcription	Gastric	stomach

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