Variant report

Variant	rs57249964
Chromosome Location	chr19:38819795-38819796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38819188..38821432-chr19:38824241..38826346,2	K562	blood:
2	chr19:38818863..38820421-chr19:38862032..38864402,2	K562	blood:
3	chr19:38793175..38794787-chr19:38818413..38820106,2	MCF-7	breast:
4	chr19:38809370..38811650-chr19:38819162..38821932,2	K562	blood:

Variant related genes	Relation type
ENSG00000099337	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10153497	1.00[AMR][1000 genomes]
rs11880285	1.00[AMR][1000 genomes]
rs11881714	1.00[AMR][1000 genomes]
rs2286548	1.00[AMR][1000 genomes]
rs2302185	1.00[AMR][1000 genomes]
rs45589333	1.00[AMR][1000 genomes]
rs57347571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57361474	1.00[AMR][1000 genomes]
rs57874113	0.86[AFR][1000 genomes]
rs58247981	1.00[AMR][1000 genomes]
rs58490212	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58591078	1.00[AMR][1000 genomes]
rs59047386	1.00[AMR][1000 genomes]
rs59776537	1.00[AMR][1000 genomes]
rs59845491	1.00[AMR][1000 genomes]
rs60068553	1.00[AMR][1000 genomes]
rs60491875	1.00[AMR][1000 genomes]
rs61648033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38811200-38826200	Weak transcription	Brain Anterior Caudate	brain
2	chr19:38811200-38826600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:38811400-38825600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:38811600-38819800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr19:38811800-38823000	Weak transcription	Brain Angular Gyrus	brain
6	chr19:38812000-38826000	Weak transcription	Fetal Thymus	thymus
7	chr19:38812000-38826600	Weak transcription	HUVEC	blood vessel
8	chr19:38812200-38823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:38812200-38826400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:38812200-38826600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:38812400-38826400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:38812400-38826400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:38812400-38826400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:38812600-38826200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:38813000-38826000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:38813000-38826400	Weak transcription	Stomach Mucosa	stomach
17	chr19:38813200-38826800	Weak transcription	Fetal Heart	heart
18	chr19:38813400-38826000	Weak transcription	Fetal Intestine Large	intestine
19	chr19:38814000-38820600	Strong transcription	Aorta	Aorta
20	chr19:38814000-38826400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:38814200-38820600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:38814200-38826400	Weak transcription	Right Atrium	heart
23	chr19:38814600-38820000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:38814600-38822800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:38814600-38826400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:38814800-38820400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr19:38815000-38822800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr19:38815000-38826400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:38815200-38820600	Strong transcription	Esophagus	oesophagus
30	chr19:38815200-38820800	Strong transcription	Ovary	ovary
31	chr19:38815600-38820600	Strong transcription	NHEK	skin
32	chr19:38815800-38822600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:38816000-38821800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:38816200-38820600	Strong transcription	Gastric	stomach
35	chr19:38816400-38820400	Strong transcription	Placenta	Placenta
36	chr19:38816600-38822000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:38816800-38820600	Strong transcription	NHLF	lung
38	chr19:38817000-38820400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:38818000-38826600	Weak transcription	Small Intestine	intestine
40	chr19:38818200-38826600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:38818400-38826000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:38818400-38826200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:38818400-38826600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:38818600-38826200	Weak transcription	Thymus	Thymus
45	chr19:38818600-38826400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:38818600-38826600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:38818800-38820400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:38818800-38825800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:38818800-38826000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:38818800-38826000	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links