Variant report

Variant	rs10425652
Chromosome Location	chr19:39986005-39986006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:39985992-39986222	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39982701..39986911-chr19:39987055..39990908,4	MCF-7	breast:

Variant related genes	Relation type
DLL3	TF binding region
ENSG00000090932	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10426543	0.84[CHB][hapmap]
rs11882744	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs1529733	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs1865093	1.00[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs3786950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802030	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4802032	1.00[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs4802033	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803248	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803254	0.94[ASW][hapmap]
rs62120691	0.82[ASN][1000 genomes]
rs8106642	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs958728	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	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
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10425652	NUMBL	cis	parietal	SCAN
rs10425652	RPS16	cis	lymphoblastoid	seeQTL
rs10425652	BSPH1	cis	parietal	SCAN
rs10425652	CEACAM6	cis	cerebellum	SCAN
rs10425652	LYPD5	cis	cerebellum	SCAN
rs10425652	APOE	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
3	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
4	chr19:39980000-39988600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:39980600-39988600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:39980800-39986600	Weak transcription	NHLF	lung
7	chr19:39980800-39988200	Weak transcription	HUVEC	blood vessel
8	chr19:39980800-39988400	Weak transcription	K562	blood
9	chr19:39981000-39986200	Weak transcription	HepG2	liver
10	chr19:39981000-39986600	Weak transcription	NH-A	brain
11	chr19:39981000-39988200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:39981000-39988400	Weak transcription	Aorta	Aorta
13	chr19:39981000-39988400	Weak transcription	GM12878-XiMat	blood
14	chr19:39981000-39988400	Weak transcription	HSMMtube	muscle
15	chr19:39981000-39988600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:39981000-39988600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:39981000-39988600	Weak transcription	Gastric	stomach
18	chr19:39981000-39988800	Weak transcription	Pancreas	Pancrea
19	chr19:39981200-39988400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:39981400-39986200	Weak transcription	Dnd41	blood
21	chr19:39981400-39986600	Weak transcription	Fetal Thymus	thymus
22	chr19:39981400-39988200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr19:39981400-39988400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:39981400-39988600	Weak transcription	Primary B cells from cord blood	blood
25	chr19:39981400-39988600	Weak transcription	HSMM	muscle
26	chr19:39981600-39986800	Weak transcription	Osteobl	bone
27	chr19:39981600-39988400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39982800-39986600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:39982800-39986800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:39982800-39986800	Weak transcription	Adipose Nuclei	Adipose
31	chr19:39982800-39987600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:39983000-39986200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:39983000-39986400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:39983000-39986400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr19:39983000-39986600	Weak transcription	Fetal Intestine Small	intestine
36	chr19:39983000-39987600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:39983200-39986400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:39983200-39986600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:39983200-39986600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:39983200-39986600	Weak transcription	Primary T cells from cord blood	blood
41	chr19:39983200-39986600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:39983200-39986600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:39983200-39986800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:39983200-39986800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr19:39983200-39988000	Weak transcription	Liver	Liver
46	chr19:39983200-39988400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:39983200-39988400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:39983200-39988400	Weak transcription	Fetal Brain Female	brain
49	chr19:39983200-39988400	Weak transcription	Spleen	Spleen
50	chr19:39983200-39988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links