Variant report

Variant	rs2873913
Chromosome Location	chr19:39629902-39629903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr19:39629256-39630454	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr19:39629879-39630408	H1-hESC	embryonic stem cell:	n/a	n/a
3	EP300	chr19:39629606-39631875	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39628877..39631480-chr19:39652977..39654703,2	K562	blood:
2	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
3	chr19:39628513..39631605-chr19:39651561..39654703,3	K562	blood:
4	chr19:39627514..39630051-chr19:39655173..39657511,2	MCF-7	breast:
5	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269172	TF binding region
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1077457	0.91[ASN][1000 genomes]
rs1079442	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083509	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083510	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610624	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12611361	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12611365	1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12611376	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12984418	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17722300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795295	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082417	0.81[ASN][1000 genomes]
rs34058542	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34110379	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34270590	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34326918	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34808880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34846983	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35163943	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35591784	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36148214	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3889485	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55748546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61171111	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67248178	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71356838	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71356839	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71356840	0.92[EUR][1000 genomes]
rs71356841	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs737450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39630800	Weak transcription	Primary T cells from cord blood	blood
2	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
3	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
6	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:39620000-39630000	Weak transcription	HepG2	liver
8	chr19:39622400-39635200	Weak transcription	Fetal Brain Female	brain
9	chr19:39622600-39639600	Weak transcription	HSMM	muscle
10	chr19:39623000-39635200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39623600-39630200	Weak transcription	Brain Angular Gyrus	brain
13	chr19:39623800-39630200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr19:39624000-39647000	Weak transcription	NHLF	lung
15	chr19:39624200-39630200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr19:39624200-39634800	Weak transcription	Fetal Kidney	kidney
17	chr19:39624400-39630200	Weak transcription	Liver	Liver
18	chr19:39624600-39630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:39624800-39632600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr19:39624800-39633000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr19:39625000-39630000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:39626600-39631000	Enhancers	Spleen	Spleen
23	chr19:39626800-39631200	Enhancers	Brain Substantia Nigra	brain
24	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:39627400-39630200	Weak transcription	Small Intestine	intestine
26	chr19:39627400-39632000	Enhancers	Brain Germinal Matrix	brain
27	chr19:39627600-39630000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:39627600-39630400	Weak transcription	HUVEC	blood vessel
29	chr19:39627600-39634400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:39627600-39635000	Weak transcription	NHEK	skin
31	chr19:39627600-39641200	Weak transcription	Hela-S3	cervix
32	chr19:39627600-39645800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr19:39628000-39630200	Weak transcription	Adipose Nuclei	Adipose
34	chr19:39628200-39630000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:39628600-39630600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr19:39628600-39631000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:39628600-39631800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:39628800-39631000	Enhancers	Stomach Mucosa	stomach
39	chr19:39628800-39631200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:39628800-39631200	Enhancers	Brain Hippocampus Middle	brain
41	chr19:39628800-39631600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr19:39628800-39631800	Genic enhancers	A549	lung
43	chr19:39628800-39632000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr19:39628800-39633600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:39629000-39630600	Enhancers	Esophagus	oesophagus
46	chr19:39629000-39630800	Enhancers	Pancreas	Pancrea
47	chr19:39629000-39631000	Enhancers	Fetal Brain Male	brain
48	chr19:39629000-39631000	Enhancers	Gastric	stomach
49	chr19:39629000-39631200	Enhancers	Brain Cingulate Gyrus	brain
50	chr19:39629000-39631200	Enhancers	Brain Inferior Temporal Lobe	brain

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