Variant report

Variant	rs1808372
Chromosome Location	chr5:167894598-167894599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:167893756..167895862-chr5:167912088..167914679,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113643	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10035471	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10036266	1.00[EUR][1000 genomes]
rs10037118	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10037130	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10038320	1.00[AMR][1000 genomes]
rs10038390	0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10038391	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040943	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10042188	1.00[AMR][1000 genomes]
rs10042576	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10044536	1.00[EUR][1000 genomes]
rs10054916	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055507	1.00[AMR][1000 genomes]
rs10056428	1.00[AMR][1000 genomes]
rs10059019	1.00[AMR][1000 genomes]
rs10063775	1.00[AMR][1000 genomes]
rs1006513	1.00[AMR][1000 genomes]
rs10068535	1.00[AMR][1000 genomes]
rs10070122	1.00[AMR][1000 genomes]
rs10075191	1.00[AMR][1000 genomes]
rs10475875	1.00[AMR][1000 genomes]
rs1108517	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12109088	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13354276	1.00[AMR][1000 genomes]
rs13359254	1.00[AMR][1000 genomes]
rs13361044	1.00[AMR][1000 genomes]
rs13361202	1.00[AMR][1000 genomes]
rs17070328	1.00[AMR][1000 genomes]
rs2010076	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28369637	1.00[AMR][1000 genomes]
rs28450630	1.00[AMR][1000 genomes]
rs28702465	1.00[AMR][1000 genomes]
rs34990715	1.00[EUR][1000 genomes]
rs55689120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55736269	1.00[AMR][1000 genomes]
rs58840409	0.87[AFR][1000 genomes]
rs61067865	1.00[AMR][1000 genomes]
rs61456455	1.00[AMR][1000 genomes]
rs6886460	1.00[AMR][1000 genomes]
rs73390783	1.00[EUR][1000 genomes]
rs73390790	1.00[EUR][1000 genomes]
rs73801875	1.00[AMR][1000 genomes]
rs73801876	1.00[AMR][1000 genomes]
rs73802326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73802328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73802340	1.00[AMR][1000 genomes]
rs73802348	1.00[AMR][1000 genomes]
rs888775	0.88[YRI][hapmap];0.96[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023985	chr5:167756193-168285807	Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv537941	chr5:167756193-168285807	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv3444818	chr5:167770667-167902204	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv970006	chr5:167870237-167924444	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167812600-167896400	Weak transcription	Colonic Mucosa	Colon
2	chr5:167829000-167896800	Weak transcription	Stomach Mucosa	stomach
3	chr5:167837000-167896800	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:167850800-167895600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:167852200-167900400	Strong transcription	Liver	Liver
6	chr5:167862000-167897000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:167863800-167899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:167864400-167897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:167869800-167895600	Weak transcription	NH-A	brain
10	chr5:167874600-167899600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:167875000-167896800	Weak transcription	Fetal Lung	lung
12	chr5:167876400-167902200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:167877400-167895600	Weak transcription	Osteobl	bone
14	chr5:167877600-167896800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:167877800-167894600	Weak transcription	Fetal Brain Male	brain
16	chr5:167878200-167897200	Strong transcription	Fetal Intestine Large	intestine
17	chr5:167878400-167898000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:167879000-167897400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:167879600-167897200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:167880200-167896200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr5:167880200-167900000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr5:167880400-167898200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:167880800-167897400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:167881000-167896600	Strong transcription	Fetal Brain Female	brain
25	chr5:167881200-167901800	Strong transcription	Placenta	Placenta
26	chr5:167884200-167895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:167884800-167901400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:167885000-167903000	Strong transcription	A549	lung
29	chr5:167885200-167900400	Strong transcription	Fetal Intestine Small	intestine
30	chr5:167885200-167902400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:167885400-167895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:167885600-167896800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:167885600-167900800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:167885800-167898600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:167885800-167912800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:167886000-167901000	Weak transcription	Fetal Kidney	kidney
37	chr5:167887200-167900400	Strong transcription	Gastric	stomach
38	chr5:167887400-167901400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:167887800-167895000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr5:167889600-167894800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:167890800-167896000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:167891200-167896000	Strong transcription	HepG2	liver
43	chr5:167891600-167895400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:167891600-167895600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:167891600-167898800	Weak transcription	HMEC	breast
46	chr5:167891800-167895600	Weak transcription	NHDF-Ad	bronchial
47	chr5:167892200-167895600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:167892200-167913400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr5:167892400-167895200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:167892400-167912800	Weak transcription	Brain Cingulate Gyrus	brain

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