Variant report

Variant	rs1458860
Chromosome Location	chr18:29952104-29952105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:29915109..29917928-chr18:29952038..29954321,2	MCF-7	breast:
2	chr18:29949594..29952442-chr18:30047301..30050702,3	MCF-7	breast:
3	chr18:29950469..29955579-chr18:30048383..30051595,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141441	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10502585	1.00[JPT][hapmap]
rs10502588	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10502589	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10502590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10502592	0.83[YRI][hapmap]
rs11877702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16959889	1.00[JPT][hapmap]
rs16963135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap]
rs16963169	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16963196	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16963205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963218	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963239	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963245	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963272	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963279	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963285	0.83[MKK][hapmap];0.83[YRI][hapmap]
rs16963339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16963367	1.00[JPT][hapmap]
rs16963370	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16963374	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2421455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35779665	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485446	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4499310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55866517	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56945883	1.00[EUR][1000 genomes]
rs57478295	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57613491	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59676860	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7228337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7236432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7237501	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7240587	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7240755	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73956901	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73956902	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958403	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958404	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958405	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958411	1.00[ASN][1000 genomes]
rs902950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29930200-29953600	Weak transcription	Fetal Muscle Leg	muscle
2	chr18:29932800-29954000	Weak transcription	Ovary	ovary
3	chr18:29937600-29952600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:29939000-29952800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr18:29946200-29958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:29946800-29953600	Weak transcription	Colon Smooth Muscle	Colon
7	chr18:29946800-29959000	Weak transcription	Fetal Lung	lung
8	chr18:29947000-29952400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr18:29947000-29953800	Weak transcription	Fetal Kidney	kidney
10	chr18:29947200-29957200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr18:29948200-29953400	Weak transcription	Gastric	stomach
12	chr18:29948200-29954000	Weak transcription	Aorta	Aorta
13	chr18:29948200-29954200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr18:29948400-29952400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr18:29948400-29952600	Weak transcription	Right Atrium	heart
16	chr18:29948400-29954200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr18:29948600-29952400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr18:29948600-29953600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr18:29948800-29952200	Weak transcription	Brain Anterior Caudate	brain
20	chr18:29949200-29952400	Weak transcription	Brain Angular Gyrus	brain
21	chr18:29950000-29966200	Weak transcription	Fetal Brain Female	brain
22	chr18:29950400-29952600	Weak transcription	Fetal Stomach	stomach
23	chr18:29950800-29956200	Enhancers	Stomach Mucosa	stomach
24	chr18:29951000-29952200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr18:29951000-29953600	Enhancers	Left Ventricle	heart
26	chr18:29951000-29954400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr18:29951000-29954600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr18:29951000-29955400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr18:29951000-29956000	Enhancers	Fetal Heart	heart
30	chr18:29951000-29956200	Enhancers	Duodenum Mucosa	Duodenum
31	chr18:29951200-29959200	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr18:29951400-29954200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:29951400-29954600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr18:29951400-29954600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:29951400-29954600	Enhancers	Adipose Nuclei	Adipose
36	chr18:29951400-29954600	Enhancers	Fetal Intestine Small	intestine
37	chr18:29951400-29954600	Enhancers	HMEC	breast
38	chr18:29951600-29953200	Enhancers	Brain Cingulate Gyrus	brain
39	chr18:29951600-29953200	Enhancers	Fetal Intestine Large	intestine
40	chr18:29951600-29954600	Enhancers	Brain Hippocampus Middle	brain
41	chr18:29951600-29954600	Enhancers	Brain Substantia Nigra	brain
42	chr18:29951800-29952200	Weak transcription	Right Ventricle	heart
43	chr18:29951800-29952200	Enhancers	Hela-S3	cervix
44	chr18:29951800-29952200	Enhancers	NHEK	skin
45	chr18:29951800-29952400	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr18:29951800-29952400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr18:29951800-29952400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr18:29951800-29952600	Flanking Active TSS	A549	lung
49	chr18:29951800-29952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr18:29951800-29952800	Weak transcription	Pancreas	Pancrea

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