Variant report

Variant	rs2382972
Chromosome Location	chr19:38594379-38594380
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38396839..38398379-chr19:38593196..38595560,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10460171	0.91[EUR][1000 genomes]
rs11083447	0.90[EUR][1000 genomes]
rs12459984	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12460013	0.89[ASN][1000 genomes]
rs12460188	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12461387	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12461946	0.84[ASN][1000 genomes]
rs12462587	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12971962	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12974504	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12975576	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12976860	0.83[EUR][1000 genomes]
rs12979004	0.82[ASN][1000 genomes]
rs12981412	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12982030	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12982734	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12983059	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12983497	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12984016	0.91[EUR][1000 genomes]
rs12984380	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12984864	0.91[EUR][1000 genomes]
rs12985707	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1545039	0.91[EUR][1000 genomes]
rs1962866	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2010234	0.84[EUR][1000 genomes]
rs2016074	0.90[EUR][1000 genomes]
rs2116862	0.91[EUR][1000 genomes]
rs2163817	0.87[EUR][1000 genomes]
rs2304132	0.90[EUR][1000 genomes]
rs2382973	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2569517	0.88[EUR][1000 genomes]
rs332845	0.91[EUR][1000 genomes]
rs332846	0.91[EUR][1000 genomes]
rs332854	0.83[EUR][1000 genomes]
rs332857	0.88[EUR][1000 genomes]
rs332859	0.88[EUR][1000 genomes]
rs332861	0.89[EUR][1000 genomes]
rs332862	0.83[EUR][1000 genomes]
rs332863	0.85[EUR][1000 genomes]
rs34646932	0.91[EUR][1000 genomes]
rs35467693	0.90[EUR][1000 genomes]
rs35469521	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35972455	0.90[EUR][1000 genomes]
rs3745943	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3852910	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3852911	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802230	0.83[ASN][1000 genomes]
rs4802248	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4803747	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4803805	0.90[EUR][1000 genomes]
rs4803808	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67910767	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71337549	0.92[EUR][1000 genomes]
rs7253312	0.91[EUR][1000 genomes]
rs7253633	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7258019	0.89[EUR][1000 genomes]
rs8100956	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8102589	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8107385	0.91[EUR][1000 genomes]
rs855617	0.92[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	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
4	chr19:38580400-38594800	Weak transcription	HSMMtube	muscle
5	chr19:38580600-38596000	Weak transcription	Stomach Mucosa	stomach
6	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
7	chr19:38584400-38597000	Weak transcription	Right Atrium	heart
8	chr19:38584800-38602400	Weak transcription	Fetal Brain Male	brain
9	chr19:38584800-38602400	Weak transcription	Fetal Heart	heart
10	chr19:38587000-38605400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr19:38587200-38603200	Strong transcription	Primary B cells from cord blood	blood
12	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr19:38588600-38597200	Strong transcription	Osteobl	bone
15	chr19:38588600-38604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:38588800-38606600	Strong transcription	Liver	Liver
17	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr19:38589400-38595200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38590200-38597200	Strong transcription	Gastric	stomach
20	chr19:38590200-38605200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:38590200-38605800	Strong transcription	Adipose Nuclei	Adipose
22	chr19:38590200-38606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:38590200-38606600	Strong transcription	Stomach Smooth Muscle	stomach
24	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr19:38590400-38595000	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr19:38590400-38599200	Strong transcription	Pancreas	Pancrea
27	chr19:38590400-38606400	Strong transcription	Fetal Brain Female	brain
28	chr19:38590400-38609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:38590800-38596800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:38590800-38597200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:38590800-38602800	Strong transcription	Spleen	Spleen
32	chr19:38590800-38603600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:38590800-38603800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr19:38590800-38606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38590800-38608800	Strong transcription	Fetal Intestine Small	intestine
36	chr19:38591000-38595200	Strong transcription	Fetal Muscle Leg	muscle
37	chr19:38591000-38596200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:38591000-38596200	Weak transcription	Hela-S3	cervix
39	chr19:38591000-38601800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:38591000-38605000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:38591200-38596200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:38591200-38597000	Weak transcription	HUVEC	blood vessel
43	chr19:38591200-38597200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:38591200-38597200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:38591200-38597200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:38591200-38597200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:38591200-38605800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr19:38591400-38596200	Weak transcription	NHEK	skin

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