Variant report

Variant	rs16963239
Chromosome Location	chr18:29934728-29934729
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29930256..29933123-chr18:29933358..29935857,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10502588	0.87[EUR][1000 genomes]
rs10502589	0.90[EUR][1000 genomes]
rs10502590	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11877702	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458860	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16959889	0.83[EUR][1000 genomes]
rs16963135	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16963169	0.90[EUR][1000 genomes]
rs16963196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16963205	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963218	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963230	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963245	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963272	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963275	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963279	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963339	0.91[EUR][1000 genomes]
rs16963367	0.83[EUR][1000 genomes]
rs16963370	0.83[EUR][1000 genomes]
rs16963374	0.83[EUR][1000 genomes]
rs2421455	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35779665	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485446	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4499310	0.98[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642668	0.90[EUR][1000 genomes]
rs55866517	1.00[ASN][1000 genomes]
rs56945883	0.88[EUR][1000 genomes]
rs57478295	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57613491	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58503085	0.91[EUR][1000 genomes]
rs59676860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60577454	0.85[EUR][1000 genomes]
rs7228337	0.84[EUR][1000 genomes]
rs7236432	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7237501	0.90[EUR][1000 genomes]
rs7240587	0.90[EUR][1000 genomes]
rs7240755	0.90[EUR][1000 genomes]
rs72931898	0.91[EUR][1000 genomes]
rs72933507	0.91[EUR][1000 genomes]
rs72933528	0.83[EUR][1000 genomes]
rs72933534	0.83[EUR][1000 genomes]
rs73956895	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73956901	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73956902	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958403	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958404	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958405	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73958411	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8085402	0.91[EUR][1000 genomes]
rs902950	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902951	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931494	0.98[AFR][1000 genomes];0.88[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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29921600-29938200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr18:29924200-29936800	Weak transcription	Pancreas	Pancrea
3	chr18:29924200-29937000	Weak transcription	Left Ventricle	heart
4	chr18:29926800-29951000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr18:29927200-29936800	Weak transcription	Psoas Muscle	Psoas
6	chr18:29927800-29938200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr18:29930000-29938200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr18:29930000-29938400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr18:29930000-29939600	Weak transcription	Fetal Stomach	stomach
10	chr18:29930000-29947600	Weak transcription	Esophagus	oesophagus
11	chr18:29930200-29937000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:29930200-29945400	Weak transcription	Fetal Intestine Small	intestine
13	chr18:29930200-29945600	Weak transcription	Fetal Intestine Large	intestine
14	chr18:29930200-29953600	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:29930400-29935400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr18:29930800-29935800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr18:29931200-29935600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr18:29931200-29936200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr18:29931200-29936200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr18:29931200-29948000	Weak transcription	Brain Angular Gyrus	brain
21	chr18:29931400-29935600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr18:29931400-29935800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr18:29931400-29940400	Weak transcription	Brain Substantia Nigra	brain
24	chr18:29931600-29935400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr18:29931600-29935400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr18:29931600-29935800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:29931600-29935800	Weak transcription	NH-A	brain
28	chr18:29931600-29936200	Weak transcription	NHDF-Ad	bronchial
29	chr18:29931600-29937400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr18:29931600-29942000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:29932000-29935800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr18:29932400-29935600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr18:29932600-29943600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:29932800-29935800	Weak transcription	Brain Anterior Caudate	brain
35	chr18:29932800-29938200	Weak transcription	Gastric	stomach
36	chr18:29932800-29954000	Weak transcription	Ovary	ovary
37	chr18:29933000-29948000	Weak transcription	Brain Hippocampus Middle	brain
38	chr18:29933600-29935800	Weak transcription	A549	lung
39	chr18:29933600-29939400	Weak transcription	Stomach Mucosa	stomach
40	chr18:29934200-29937200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr18:29934400-29934800	Enhancers	Aorta	Aorta
42	chr18:29934400-29934800	Enhancers	Right Ventricle	heart
43	chr18:29934400-29934800	Enhancers	Stomach Smooth Muscle	stomach
44	chr18:29934400-29935200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:29934400-29935200	Enhancers	Fetal Heart	heart
46	chr18:29934600-29934800	Enhancers	Small Intestine	intestine
47	chr18:29934600-29934800	Enhancers	HepG2	liver

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