Variant report

Variant	rs12979004
Chromosome Location	chr19:38566358-38566359
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	chr19:38546251..38550140-chr19:38563809..38566619,4	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12459984	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12460013	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12461387	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12461946	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12462587	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12971962	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12974504	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12981412	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12982030	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12982734	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12983059	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12983497	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2382972	0.82[ASN][1000 genomes]
rs2382973	0.84[ASN][1000 genomes]
rs3745943	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802230	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803747	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8102589	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:38549200-38572000	Weak transcription	Liver	Liver
6	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
7	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
10	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:38553200-38570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38553800-38572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:38554200-38572600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:38554600-38567000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr19:38554600-38570400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:38554600-38571800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:38554800-38571800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:38554800-38573200	Weak transcription	Brain Angular Gyrus	brain
23	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:38555000-38570800	Weak transcription	Fetal Intestine Large	intestine
25	chr19:38561200-38570800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr19:38561400-38570400	Weak transcription	Hela-S3	cervix
27	chr19:38561600-38567200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:38561600-38570000	Weak transcription	NHLF	lung
29	chr19:38561600-38570000	Weak transcription	Osteobl	bone
30	chr19:38561600-38570600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:38561800-38567000	Weak transcription	Pancreas	Pancrea
32	chr19:38561800-38570000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:38561800-38570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:38561800-38570200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:38561800-38570400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:38561800-38570400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:38561800-38570400	Weak transcription	Esophagus	oesophagus
38	chr19:38561800-38570400	Weak transcription	Lung	lung
39	chr19:38561800-38570400	Weak transcription	HMEC	breast
40	chr19:38561800-38570400	Weak transcription	NHEK	skin
41	chr19:38562400-38570400	Weak transcription	Placenta	Placenta
42	chr19:38562600-38570400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:38562800-38569400	Weak transcription	HSMM	muscle
44	chr19:38564000-38567000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr19:38564000-38569000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:38564000-38572400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr19:38564200-38571800	Weak transcription	Primary T cells from cord blood	blood
48	chr19:38564200-38571800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr19:38564600-38572000	Weak transcription	Fetal Brain Female	brain
50	chr19:38564800-38567000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links