Variant report

Variant	rs12425863
Chromosome Location	chr12:26190313-26190314
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	chr12:26183705..26186106-chr12:26190195..26191790,2	MCF-7	breast:
2	chr12:26186658..26189002-chr12:26189615..26191269,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10505989	0.89[AMR][1000 genomes]
rs12426668	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1495649	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1533244	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16929780	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16929815	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16929860	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16929894	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16929895	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16929904	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16929970	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16929998	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2343200	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4963644	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4963947	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57082706	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57791860	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60836137	0.83[ASN][1000 genomes]
rs61123975	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73074872	0.82[AMR][1000 genomes]
rs73074898	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077103	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73077131	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73077152	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73077161	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73077176	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73077179	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73079010	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73079021	0.81[AMR][1000 genomes]
rs73079023	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73079024	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73079069	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73080925	0.89[AMR][1000 genomes];0.82[EUR][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	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26171000-26190600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr12:26175000-26190600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:26175000-26191000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:26175200-26190800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:26180800-26195000	Weak transcription	HSMM	muscle
6	chr12:26181000-26195200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:26182200-26190600	Weak transcription	Gastric	stomach
8	chr12:26182200-26195800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:26183600-26190600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:26186000-26200400	Weak transcription	Right Ventricle	heart
11	chr12:26186200-26193400	Weak transcription	Fetal Lung	lung
12	chr12:26186200-26195000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:26186400-26191000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:26186400-26191000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:26187000-26190600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:26187000-26190600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:26187000-26190800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:26187000-26193200	Weak transcription	Esophagus	oesophagus
19	chr12:26187200-26190600	Weak transcription	Pancreas	Pancrea
20	chr12:26187200-26190600	Weak transcription	Right Atrium	heart
21	chr12:26187200-26190800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:26187200-26190800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:26187200-26193200	Weak transcription	Lung	lung
24	chr12:26187200-26195800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:26187200-26196200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:26187200-26200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:26187400-26190600	Weak transcription	Aorta	Aorta
28	chr12:26187600-26190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:26187800-26194800	Weak transcription	HUVEC	blood vessel
30	chr12:26188000-26193200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:26188000-26194600	Weak transcription	Osteobl	bone
32	chr12:26188000-26195200	Weak transcription	Fetal Kidney	kidney
33	chr12:26188200-26191800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:26188200-26192000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:26188200-26194600	Weak transcription	NHDF-Ad	bronchial
36	chr12:26188200-26194800	Weak transcription	NH-A	brain
37	chr12:26188800-26194000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:26189000-26193800	Enhancers	Fetal Intestine Small	intestine
39	chr12:26189200-26194800	Weak transcription	Hela-S3	cervix
40	chr12:26189400-26190600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:26189400-26190600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:26189600-26191200	Enhancers	Left Ventricle	heart
43	chr12:26189800-26190600	Enhancers	Brain Hippocampus Middle	brain
44	chr12:26189800-26190600	Enhancers	Brain Substantia Nigra	brain
45	chr12:26189800-26191200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr12:26189800-26192400	Enhancers	Fetal Intestine Large	intestine
47	chr12:26190000-26190400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:26190000-26190800	Enhancers	Brain Anterior Caudate	brain
49	chr12:26190000-26191000	Enhancers	Ovary	ovary
50	chr12:26190000-26191200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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