Variant report

Variant	rs10425074
Chromosome Location	chr19:45640124-45640125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45639525-45641085	GM12892	blood:	n/a	n/a
2	NFIC	chr19:45639962-45640916	GM12878	blood:	n/a	n/a
3	RUNX3	chr19:45639801-45640166	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:45639386-45641045	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:45639690-45641016	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:45639677-45640203	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:45639691-45640132	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:45639326-45641397	GM12891	blood:	n/a	n/a
9	EBF1	chr19:45639525-45641042	GM12878	blood:	n/a	chr19:45640734-45640745
10	POLR2A	chr19:45639803-45640983	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:45639224-45641087	GM12878	blood:	n/a	n/a
12	POU2F2	chr19:45639631-45640260	GM12891	blood:	n/a	n/a
13	STAT5A	chr19:45639919-45640898	GM12878	blood:	n/a	n/a
14	RUNX3	chr19:45639549-45640181	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:45639649-45641010	GM19193	blood:	n/a	n/a
16	ELF1	chr19:45639624-45640522	GM12878	blood:	n/a	n/a
17	SPI1	chr19:45639656-45640141	GM12891	blood:	n/a	n/a
18	EBF1	chr19:45640119-45640959	GM12878	blood:	n/a	chr19:45640734-45640745
19	POLR2A	chr19:45639639-45640150	GM12891	blood:	n/a	n/a
20	POLR2A	chr19:45639473-45641086	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:45639598-45640940	GM12878	blood:	n/a	n/a
22	USF2	chr19:45639688-45641111	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:45639609-45640181	GM12891	blood:	n/a	n/a
24	POLR2A	chr19:45639662-45640999	GM18951	blood:	n/a	n/a
25	IKZF1	chr19:45639856-45640969	GM12878	blood:	n/a	n/a
26	TCF12	chr19:45639815-45640129	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:45639576-45641018	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:45639645-45641033	GM12892	blood:	n/a	n/a
29	MAZ	chr19:45639755-45640954	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:45639604-45640260	GM12891	blood:	n/a	n/a
31	MTA3	chr19:45639324-45641142	GM12878	blood:	n/a	n/a
32	SPI1	chr19:45639460-45641085	GM12878	blood:	n/a	n/a
33	CUX1	chr19:45640120-45640858	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45580675..45582484-chr19:45637452..45640125,3	MCF-7	breast:
2	chr19:45637342..45640694-chr19:45642011..45644916,3	K562	blood:
3	chr19:45639467..45643704-chr19:45647170..45652290,6	K562	blood:
4	chr19:45639686..45641880-chr19:45681901..45684356,2	MCF-7	breast:
5	chr19:45638752..45643704-chr19:45645351..45650444,8	K562	blood:
6	chr19:45628639..45633572-chr19:45633990..45640719,7	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKPD1-1	chr19:45639307-45641075	ENSG00000250044
2	lnc-NKPD1-1	chr19:45640122-45640235	ENSG00000267044.1

No data

Variant related genes	Relation type
PPP1R37	TF binding region
ENSG00000104866	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000267346	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000267545	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1005451	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10401157	0.97[ASN][1000 genomes]
rs10401823	0.94[ASN][1000 genomes]
rs10403214	0.80[YRI][hapmap]
rs10408847	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10413253	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10416500	0.87[ASN][1000 genomes]
rs10420562	0.92[ASN][1000 genomes]
rs10421932	0.88[YRI][hapmap]
rs1048699	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1114831	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1114832	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12459074	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462040	0.97[ASN][1000 genomes]
rs17643262	0.83[CHD][hapmap]
rs2004357	0.97[ASN][1000 genomes]
rs2041262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28469095	0.92[ASN][1000 genomes]
rs28620490	0.97[ASN][1000 genomes]
rs34545713	0.97[ASN][1000 genomes]
rs3925162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57565080	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248421	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10425074	Hs.466924	cis	multi-tissue	Pritchard
rs10425074	KLK9	cis	parietal	SCAN
rs10425074	AP2S1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45610400-45644400	Weak transcription	Aorta	Aorta
2	chr19:45617000-45651600	Weak transcription	Fetal Kidney	kidney
3	chr19:45620800-45643800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:45621200-45644000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr19:45621600-45643800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:45625000-45654200	Weak transcription	NHDF-Ad	bronchial
7	chr19:45626200-45644400	Weak transcription	Ovary	ovary
8	chr19:45626200-45653400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:45627600-45655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:45627800-45644000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr19:45629400-45644000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:45629600-45643800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:45629600-45644600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:45629800-45643800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:45629800-45643800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:45629800-45644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:45630000-45641400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:45630800-45653200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr19:45631800-45641400	Strong transcription	Fetal Stomach	stomach
20	chr19:45632600-45643000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:45632600-45643400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr19:45632600-45643600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:45633600-45643000	Weak transcription	Lung	lung
24	chr19:45633600-45655200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:45633800-45642800	Weak transcription	Dnd41	blood
26	chr19:45634200-45641400	Strong transcription	Fetal Intestine Small	intestine
27	chr19:45634200-45644400	Weak transcription	NHEK	skin
28	chr19:45634200-45645000	Weak transcription	HUVEC	blood vessel
29	chr19:45634400-45641200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:45634400-45641600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:45634400-45653000	Weak transcription	NH-A	brain
32	chr19:45634600-45641400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:45634600-45641400	Weak transcription	Esophagus	oesophagus
34	chr19:45636600-45641800	Enhancers	Primary B cells from peripheral blood	blood
35	chr19:45637000-45641600	Enhancers	Primary B cells from cord blood	blood
36	chr19:45637200-45640600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:45637400-45640600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:45637400-45640600	Weak transcription	Thymus	Thymus
39	chr19:45637400-45644000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr19:45637400-45644200	Weak transcription	Primary T cells from cord blood	blood
41	chr19:45638000-45642000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr19:45638400-45640400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:45638600-45640600	Enhancers	Brain Cingulate Gyrus	brain
44	chr19:45638600-45640600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr19:45638600-45641800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:45638600-45642000	Enhancers	Fetal Muscle Leg	muscle
47	chr19:45638800-45640800	Weak transcription	Fetal Intestine Large	intestine
48	chr19:45638800-45652400	Weak transcription	Small Intestine	intestine
49	chr19:45639200-45640400	Enhancers	HepG2	liver
50	chr19:45639200-45640800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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