Variant report

Variant	rs12984380
Chromosome Location	chr19:38595491-38595492
allele	A/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
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

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

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

rs_ID	r²[population]
rs10460171	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083447	0.86[EUR][1000 genomes]
rs12459984	0.85[AFR][1000 genomes]
rs12460188	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12461387	0.80[ASN][1000 genomes]
rs12971962	0.81[AFR][1000 genomes]
rs12974504	0.80[ASN][1000 genomes]
rs12975576	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12981412	0.80[ASN][1000 genomes]
rs12982030	0.83[ASN][1000 genomes]
rs12982734	0.82[ASN][1000 genomes]
rs12983059	0.80[ASN][1000 genomes]
rs12983497	0.80[ASN][1000 genomes]
rs12984016	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12984864	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12985707	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545039	0.87[EUR][1000 genomes]
rs1962866	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2004981	0.83[EUR][1000 genomes]
rs2010234	0.80[EUR][1000 genomes]
rs2016074	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2116862	0.87[EUR][1000 genomes]
rs2163817	0.83[EUR][1000 genomes]
rs2304132	0.86[EUR][1000 genomes]
rs2382972	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2382973	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2569517	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332845	0.87[EUR][1000 genomes]
rs332846	0.87[EUR][1000 genomes]
rs332857	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332859	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332861	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs332862	0.80[ASN][1000 genomes]
rs332863	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34646932	0.87[EUR][1000 genomes]
rs35467693	0.86[EUR][1000 genomes]
rs35469521	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35972455	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3852910	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3852911	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802248	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803747	0.84[AFR][1000 genomes]
rs4803805	0.86[EUR][1000 genomes]
rs4803808	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67910767	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71337549	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7253312	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7253633	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7258019	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8100956	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8102589	0.84[AFR][1000 genomes]
rs8107385	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855617	0.88[EUR][1000 genomes];0.83[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: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	chr19:38580600-38596000	Weak transcription	Stomach Mucosa	stomach
5	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
6	chr19:38584400-38597000	Weak transcription	Right Atrium	heart
7	chr19:38584800-38602400	Weak transcription	Fetal Brain Male	brain
8	chr19:38584800-38602400	Weak transcription	Fetal Heart	heart
9	chr19:38587000-38605400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr19:38587200-38603200	Strong transcription	Primary B cells from cord blood	blood
11	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr19:38588600-38597200	Strong transcription	Osteobl	bone
14	chr19:38588600-38604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:38588800-38606600	Strong transcription	Liver	Liver
16	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr19:38590200-38597200	Strong transcription	Gastric	stomach
18	chr19:38590200-38605200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:38590200-38605800	Strong transcription	Adipose Nuclei	Adipose
20	chr19:38590200-38606600	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:38590200-38606600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:38590400-38599200	Strong transcription	Pancreas	Pancrea
24	chr19:38590400-38606400	Strong transcription	Fetal Brain Female	brain
25	chr19:38590400-38609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:38590800-38596800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:38590800-38597200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:38590800-38602800	Strong transcription	Spleen	Spleen
29	chr19:38590800-38603600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:38590800-38603800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr19:38590800-38606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:38590800-38608800	Strong transcription	Fetal Intestine Small	intestine
33	chr19:38591000-38596200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:38591000-38596200	Weak transcription	Hela-S3	cervix
35	chr19:38591000-38601800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:38591000-38605000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:38591200-38596200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr19:38591200-38597000	Weak transcription	HUVEC	blood vessel
39	chr19:38591200-38597200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:38591200-38597200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:38591200-38597200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:38591200-38597200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:38591200-38605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:38591200-38605800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:38591400-38596200	Weak transcription	NHEK	skin
47	chr19:38591400-38600800	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:38591400-38603600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr19:38591400-38605400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:38591600-38597200	Strong transcription	A549	lung

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