Variant report

Variant	rs1368469
Chromosome Location	chr19:40024364-40024365
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr19:40024122-40024469	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr19:40022001-40025161	A549	lung:	n/a	n/a
3	SIN3AK20	chr19:40022173-40025671	PANC-1	pancreas:	n/a	n/a
4	CTCF	chr19:40024240-40024390	GM12872	blood:	n/a	n/a
5	REST	chr19:40022447-40024770	PANC-1	pancreas:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39988241..39989038-chr19:40023625..40024451,2	MCF-7	breast:
2	chr19:39934791..39938517-chr19:40022234..40026334,4	K562	blood:
3	chr19:39963222..39966724-chr19:40022598..40024872,4	K562	blood:
4	chr19:39934545..39937545-chr19:40023023..40025430,4	MCF-7	breast:
5	chr19:39880509..39882503-chr19:40021734..40025038,3	K562	blood:
6	chr19:39880299..39881893-chr19:40023517..40025617,2	K562	blood:
7	chr19:39961748..39964722-chr19:40022955..40025016,3	K562	blood:
8	chr19:39923160..39926894-chr19:40022027..40025011,8	K562	blood:
9	chr19:39925075..39926642-chr19:40022135..40025107,3	K562	blood:
10	chr19:40023614..40026391-chr19:40028689..40031990,5	MCF-7	breast:
11	chr19:39969762..39972823-chr19:40020818..40024781,5	K562	blood:
12	chr19:39930777..39932408-chr19:40023425..40025081,2	K562	blood:
13	chr19:39988746..39992361-chr19:40020493..40024366,5	MCF-7	breast:
14	chr19:39898615..39904728-chr19:40019936..40025504,8	K562	blood:
15	chr19:40019907..40024445-chr19:40029285..40031709,4	MCF-7	breast:

No data

Variant related genes	Relation type
EID2B	TF binding region
TDGF1P7	TF binding region
ENSG00000176396	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000090932	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000006712	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12608773	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12610740	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610751	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12610833	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12611125	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12972285	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12972675	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12973775	0.84[AMR][1000 genomes]
rs12978311	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12980249	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17795475	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34271968	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34856311	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34885802	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35038530	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4803258	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803259	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55994613	0.84[AMR][1000 genomes]
rs59485553	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs60587381	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7247184	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7247218	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7257553	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7257904	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7258348	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv911694	chr19:40015907-40031369	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv137930	chr19:40019489-40027856	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40023400-40025400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:40023600-40025200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:40023600-40025800	Enhancers	K562	blood
4	chr19:40023600-40027000	Weak transcription	Fetal Lung	lung
5	chr19:40023600-40028800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:40023600-40028800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:40023600-40029000	Weak transcription	NHDF-Ad	bronchial
8	chr19:40023600-40029200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:40023600-40029200	Weak transcription	HSMM	muscle
10	chr19:40023600-40029800	Weak transcription	Aorta	Aorta
11	chr19:40023600-40029800	Weak transcription	Left Ventricle	heart
12	chr19:40023800-40028400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:40023800-40028400	Weak transcription	GM12878-XiMat	blood
14	chr19:40023800-40028600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:40023800-40028800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:40023800-40028800	Weak transcription	Brain Substantia Nigra	brain
17	chr19:40023800-40028800	Weak transcription	Fetal Brain Male	brain
18	chr19:40023800-40029000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:40023800-40029000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:40023800-40029000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:40023800-40029000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr19:40023800-40029000	Weak transcription	HMEC	breast
23	chr19:40023800-40029000	Weak transcription	Osteobl	bone
24	chr19:40023800-40029200	Weak transcription	Primary B cells from cord blood	blood
25	chr19:40023800-40029200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:40023800-40029200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:40023800-40029200	Weak transcription	Adipose Nuclei	Adipose
28	chr19:40023800-40029200	Weak transcription	Fetal Brain Female	brain
29	chr19:40023800-40029200	Weak transcription	Fetal Heart	heart
30	chr19:40023800-40029200	Weak transcription	Fetal Kidney	kidney
31	chr19:40024000-40024600	Enhancers	HepG2	liver
32	chr19:40024000-40027400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr19:40024000-40028200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:40024000-40028400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:40024000-40028400	Weak transcription	Brain Anterior Caudate	brain
36	chr19:40024000-40028400	Weak transcription	Brain Germinal Matrix	brain
37	chr19:40024000-40028400	Weak transcription	Dnd41	blood
38	chr19:40024000-40028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:40024000-40028800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:40024000-40028800	Weak transcription	Liver	Liver
41	chr19:40024000-40028800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:40024000-40028800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:40024000-40029000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:40024000-40029000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr19:40024000-40029000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:40024000-40029000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:40024000-40029000	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:40024000-40029000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:40024000-40029000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:40024000-40029200	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links