Variant report

Variant	rs12460007
Chromosome Location	chr19:45656069-45656070
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr19:45655892-45656083	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr19:45655725-45656538	GM12878	blood:	n/a	n/a
3	BRCA1	chr19:45655822-45656133	H1-hESC	embryonic stem cell:	n/a	n/a
4	RUNX3	chr19:45655821-45656400	GM12878	blood:	n/a	n/a
5	E2F6	chr19:45655175-45657423	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr19:45655759-45656254	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:45655508-45656445	GM12878	blood:	n/a	n/a
8	TEAD4	chr19:45655651-45656176	H1-hESC	embryonic stem cell:	n/a	n/a
9	GABPA	chr19:45655169-45656476	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:45655365-45656375	A549	lung:	n/a	n/a
11	MAX	chr19:45655717-45657117	GM12878	blood:	n/a	chr19:45657081-45657091
12	MAX	chr19:45655239-45657363	H1-hESC	embryonic stem cell:	n/a	chr19:45657081-45657091
13	MTA3	chr19:45655898-45656408	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:45655747-45656232	GM12892	blood:	n/a	n/a
15	MXI1	chr19:45654849-45658095	IMR90	lung:	n/a	chr19:45657939-45657948 chr19:45657937-45657946
16	GABPA	chr19:45654975-45656327	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr19:45655746-45656091	HUVEC	blood vessel:	n/a	n/a
18	RAD21	chr19:45655604-45656098	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:45655707-45656301	H1-neurons	neurons:	n/a	n/a
20	MAX	chr19:45655655-45656267	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr19:45655762-45656365	H1-hESC	embryonic stem cell:	n/a	n/a
22	CREB1	chr19:45655550-45656311	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr19:45655414-45657598	SK-N-SH	brain:	n/a	n/a
24	CREB1	chr19:45655414-45656269	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr19:45655290-45657356	H1-hESC	embryonic stem cell:	n/a	chr19:45657081-45657091
26	POLR2A	chr19:45655329-45656481	GM12878	blood:	n/a	n/a
27	TCF12	chr19:45655850-45656112	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:45655666-45656498	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr19:45655773-45656267	H1-neurons	neurons:	n/a	n/a
30	MAX	chr19:45655622-45656571	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr19:45655840-45656132	GM12878	blood:	n/a	n/a
32	ELF1	chr19:45655813-45656610	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:45653572-45656097	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr19:45655528-45656307	A549	lung:	n/a	n/a
35	TCF3	chr19:45655556-45656190	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:45655259-45656957	GM12878	blood:	n/a	n/a
37	MAX	chr19:45655766-45657142	HUVEC	blood vessel:	n/a	chr19:45657081-45657091
38	MYC	chr19:45655796-45656504	GM12878	blood:	n/a	n/a
39	E2F6	chr19:45655264-45657260	H1-hESC	embryonic stem cell:	n/a	n/a
40	PAX5	chr19:45655958-45656113	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45655086..45657605-chr19:45680853..45682730,2	MCF-7	breast:
2	chr19:45651718..45653898-chr19:45656029..45658572,2	K562	blood:
3	chr19:45654421..45658397-chr19:45679888..45682724,3	K562	blood:
4	chr19:45640971..45644367-chr19:45655076..45659170,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267037	TF binding region
ENSG00000189114	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000267037	Chromatin interaction
ENSG00000104866	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10406911	0.86[ASW][hapmap];0.81[MKK][hapmap]
rs10408462	0.86[ASW][hapmap]
rs10420443	1.00[AMR][1000 genomes]
rs10425380	0.86[ASW][hapmap]
rs1076384	0.86[ASW][hapmap]
rs12459386	0.86[ASW][hapmap];0.80[MKK][hapmap]
rs12459402	0.92[AFR][1000 genomes]
rs12459851	1.00[AMR][1000 genomes]
rs12460771	1.00[AMR][1000 genomes]
rs61531804	0.92[AFR][1000 genomes]
rs754365	1.00[YRI][hapmap];0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv3347313	chr19:45654737-45657285	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45639800-45656800	Weak transcription	K562	blood
2	chr19:45650800-45656800	Weak transcription	Dnd41	blood
3	chr19:45651800-45660200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:45654600-45657200	Bivalent Enhancer	Fetal Intestine Small	intestine
5	chr19:45654600-45658000	Bivalent Enhancer	Placenta	Placenta
6	chr19:45654800-45656200	Weak transcription	A549	lung
7	chr19:45654800-45656400	Bivalent Enhancer	Lung	lung
8	chr19:45654800-45657200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:45654800-45657200	Weak transcription	Hela-S3	cervix
10	chr19:45654800-45657400	Bivalent Enhancer	Fetal Brain Male	brain
11	chr19:45654800-45660400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:45655000-45656200	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr19:45655000-45656800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
14	chr19:45655000-45656800	Bivalent Enhancer	NHLF	lung
15	chr19:45655000-45657400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:45655000-45657400	Enhancers	Fetal Heart	heart
17	chr19:45655000-45657400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
18	chr19:45655000-45657600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:45655200-45657400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr19:45655200-45657400	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr19:45655200-45657400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr19:45655200-45657400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:45655200-45657400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr19:45655200-45657400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:45655200-45657400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
26	chr19:45655200-45658000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:45655400-45656200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:45655400-45656200	Enhancers	Liver	Liver
29	chr19:45655400-45656800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr19:45655400-45656800	Enhancers	Right Atrium	heart
31	chr19:45655400-45656800	Weak transcription	HepG2	liver
32	chr19:45655400-45657000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:45655400-45657200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:45655400-45657200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:45655400-45657200	Flanking Active TSS	Right Ventricle	heart
36	chr19:45655400-45657400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr19:45655400-45657400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:45655400-45657400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
39	chr19:45655400-45657400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
40	chr19:45655600-45656200	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
41	chr19:45655600-45656200	Bivalent Enhancer	NH-A	brain
42	chr19:45655600-45656200	Bivalent Enhancer	NHDF-Ad	bronchial
43	chr19:45655600-45656400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:45655600-45656600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:45655600-45656600	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr19:45655600-45656800	Bivalent Enhancer	HMEC	breast
47	chr19:45655600-45656800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
48	chr19:45655600-45657000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:45655600-45657000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
50	chr19:45655600-45657000	Flanking Active TSS	Brain Angular Gyrus	brain

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