Variant report

Variant	rs11800001
Chromosome Location	chr1:153870850-153870851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153869297..153871821-chr1:153893470..153896495,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143614	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10127484	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908512	0.88[EUR][1000 genomes]
rs10908525	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908526	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264573	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264621	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264736	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1139620	0.86[ASN][1000 genomes]
rs12120118	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12124424	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130611	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133492	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12142639	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142733	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738361	0.86[ASN][1000 genomes]
rs2252508	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35711150	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276953	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4341393	0.86[ASN][1000 genomes]
rs4370789	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4451582	0.83[ASN][1000 genomes]
rs4540690	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4581307	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4596938	0.86[ASN][1000 genomes]
rs61803655	0.86[ASN][1000 genomes]
rs6427300	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427306	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661009	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668066	0.86[ASN][1000 genomes]
rs6671362	0.82[AMR][1000 genomes]
rs72694233	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7414227	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415004	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522030	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7549032	0.84[EUR][1000 genomes]
rs7554469	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9426935	0.86[ASN][1000 genomes]
rs9426938	0.86[ASN][1000 genomes]
rs9427232	0.86[ASN][1000 genomes]
rs9427233	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
4	chr1:153846400-153871600	Weak transcription	Lung	lung
5	chr1:153853800-153892200	Weak transcription	Pancreas	Pancrea
6	chr1:153853800-153893400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:153854000-153892600	Weak transcription	Colonic Mucosa	Colon
8	chr1:153854400-153876200	Weak transcription	Spleen	Spleen
9	chr1:153854400-153892400	Weak transcription	Aorta	Aorta
10	chr1:153854600-153892200	Weak transcription	HSMM	muscle
11	chr1:153854800-153871200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:153855000-153886800	Weak transcription	Gastric	stomach
13	chr1:153855000-153886800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:153855000-153887200	Weak transcription	Ovary	ovary
15	chr1:153855000-153891800	Weak transcription	NHEK	skin
16	chr1:153855000-153892400	Weak transcription	NHLF	lung
17	chr1:153855000-153892800	Weak transcription	NH-A	brain
18	chr1:153855200-153871200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:153855200-153871200	Weak transcription	Fetal Brain Female	brain
20	chr1:153855200-153880600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:153855400-153871200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:153855400-153876400	Weak transcription	Osteobl	bone
23	chr1:153855400-153879600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:153855400-153892000	Weak transcription	HMEC	breast
25	chr1:153855600-153871200	Weak transcription	HUVEC	blood vessel
26	chr1:153855600-153873600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:153855600-153892200	Weak transcription	Fetal Kidney	kidney
28	chr1:153856000-153871400	Weak transcription	Brain Germinal Matrix	brain
29	chr1:153856000-153890400	Weak transcription	Brain Angular Gyrus	brain
30	chr1:153856000-153891600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:153859000-153873600	Strong transcription	Fetal Thymus	thymus
32	chr1:153860000-153890400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:153860200-153879400	Weak transcription	A549	lung
34	chr1:153861200-153871000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:153861200-153891600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:153861200-153892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:153861400-153873600	Weak transcription	Brain Substantia Nigra	brain
38	chr1:153861400-153877000	Weak transcription	NHDF-Ad	bronchial
39	chr1:153861400-153890800	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:153861600-153873000	Weak transcription	Brain Anterior Caudate	brain
41	chr1:153861600-153873600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:153861600-153877200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:153861600-153879400	Weak transcription	Fetal Lung	lung
44	chr1:153861800-153871000	Weak transcription	Adipose Nuclei	Adipose
45	chr1:153861800-153871200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:153861800-153871600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:153861800-153875800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:153861800-153875800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:153862000-153871400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:153862000-153872600	Strong transcription	Monocytes-CD14+_RO01746	blood

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