Variant report

Variant	rs16963225
Chromosome Location	chr18:29932387-29932388
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	chr18:29930256..29933123-chr18:29933358..29935857,3	MCF-7	breast:
2	chr18:29931862..29933961-chr18:29952330..29954097,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10502585	1.00[JPT][hapmap]
rs10502588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs10502589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs10502590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	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]
rs16959889	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs16963135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16963169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs16963196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16963205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];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]
rs16963230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963239	0.96[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	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[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[JPT][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs16963367	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs16963370	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs16963374	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2421455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[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[MKK][hapmap];0.91[YRI][hapmap];0.86[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	0.94[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	0.98[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60577454	0.85[EUR][1000 genomes]
rs7228337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7236432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7237501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.90[EUR][1000 genomes]
rs7240587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.90[EUR][1000 genomes]
rs7240755	1.00[CEU][hapmap];1.00[CHB][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[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:49 , 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	chr18:29928800-29933000	Enhancers	Colon Smooth Muscle	Colon
8	chr18:29929000-29932400	Enhancers	Rectal Smooth Muscle	rectum
9	chr18:29929000-29933600	Enhancers	Fetal Kidney	kidney
10	chr18:29930000-29938200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr18:29930000-29938400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:29930000-29939600	Weak transcription	Fetal Stomach	stomach
13	chr18:29930000-29947600	Weak transcription	Esophagus	oesophagus
14	chr18:29930200-29933600	Enhancers	Stomach Mucosa	stomach
15	chr18:29930200-29934400	Weak transcription	Right Ventricle	heart
16	chr18:29930200-29937000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:29930200-29945400	Weak transcription	Fetal Intestine Small	intestine
18	chr18:29930200-29945600	Weak transcription	Fetal Intestine Large	intestine
19	chr18:29930200-29953600	Weak transcription	Fetal Muscle Leg	muscle
20	chr18:29930400-29932800	Weak transcription	HepG2	liver
21	chr18:29930400-29934400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr18:29930400-29935400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr18:29930800-29934400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr18:29930800-29934400	Weak transcription	Aorta	Aorta
25	chr18:29930800-29935800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr18:29931200-29932800	Weak transcription	A549	lung
27	chr18:29931200-29934400	Weak transcription	Fetal Heart	heart
28	chr18:29931200-29935600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:29931200-29936200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:29931200-29936200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr18:29931200-29948000	Weak transcription	Brain Angular Gyrus	brain
32	chr18:29931400-29932400	Weak transcription	Brain Hippocampus Middle	brain
33	chr18:29931400-29935600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr18:29931400-29935800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr18:29931400-29940400	Weak transcription	Brain Substantia Nigra	brain
36	chr18:29931600-29935400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr18:29931600-29935400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr18:29931600-29935800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr18:29931600-29935800	Weak transcription	NH-A	brain
40	chr18:29931600-29936200	Weak transcription	NHDF-Ad	bronchial
41	chr18:29931600-29937400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr18:29931600-29942000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr18:29932000-29932600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr18:29932000-29932600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr18:29932000-29935800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr18:29932200-29932400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr18:29932200-29932800	Enhancers	Brain Anterior Caudate	brain
48	chr18:29932200-29932800	Enhancers	Gastric	stomach
49	chr18:29932200-29932800	Enhancers	Ovary	ovary

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