Variant report

Variant	rs12489907
Chromosome Location	chr3:19990368-19990369
allele	C/T
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	CUX1	chr3:19989021-19990564	K562	blood:	n/a	n/a
2	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:19986265-20000717	K562	blood:	n/a	n/a
4	POLR2A	chr3:19990061-19991082	GM12878	blood:	n/a	n/a
5	IRF1	chr3:19986493-19990740	K562	blood:	n/a	chr3:19990060-19990067 chr3:19987995-19988009 chr3:19988390-19988404
6	POLR2A	chr3:19987841-19990881	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
4	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
5	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
6	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

Variant related genes	Relation type
RAB5A	TF binding region
EFHB	TF binding region
ENSG00000144566	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11716116	0.92[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12486406	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496946	0.91[ASN][1000 genomes]
rs13078869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13079277	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098043	0.88[ASN][1000 genomes]
rs13098054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2170342	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2623078	0.83[CHB][hapmap]
rs2686325	0.84[CEU][hapmap]
rs2948104	0.84[CHB][hapmap]
rs34050713	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34468236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34955379	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35094497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35172759	0.91[ASN][1000 genomes]
rs35757621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4302401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4858660	0.90[ASN][1000 genomes]
rs6778866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781143	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7625149	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9968122	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:19987200-19990400	Active TSS	Placenta	Placenta
3	chr3:19987200-19990600	Active TSS	K562	blood
4	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:19987400-19990400	Active TSS	NHDF-Ad	bronchial
6	chr3:19987400-19990800	Active TSS	Right Atrium	heart
7	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
8	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:19987600-19990400	Active TSS	Colonic Mucosa	Colon
10	chr3:19987600-19990400	Active TSS	Fetal Kidney	kidney
11	chr3:19987600-19990800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:19987600-19991000	Active TSS	NHLF	lung
13	chr3:19987600-19991600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:19987800-19990400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:19987800-19990400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:19987800-19990800	Active TSS	Psoas Muscle	Psoas
17	chr3:19987800-19990800	Active TSS	Right Ventricle	heart
18	chr3:19987800-19991400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:19987800-19991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:19988000-19990400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:19988000-19990400	Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:19988000-19990400	Active TSS	NHEK	skin
23	chr3:19988000-19990600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:19988000-19990600	Active TSS	Stomach Smooth Muscle	stomach
25	chr3:19988000-19990600	Active TSS	HMEC	breast
26	chr3:19988000-19990800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:19988000-19991200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr3:19988000-19991400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:19988200-19990400	Active TSS	Fetal Intestine Large	intestine
30	chr3:19988200-19990400	Active TSS	Fetal Stomach	stomach
31	chr3:19988200-19990400	Active TSS	NH-A	brain
32	chr3:19988200-19990600	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:19988200-19990800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:19988200-19990800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr3:19988200-19990800	Active TSS	Fetal Muscle Leg	muscle
36	chr3:19988200-19991600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:19988200-19991600	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:19989000-19990800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr3:19989400-19990400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:19989400-19990400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:19989400-19990600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:19989400-19990600	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr3:19989400-19990600	Active TSS	HepG2	liver
44	chr3:19989400-19990800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:19989400-19991000	Flanking Active TSS	Fetal Brain Female	brain
46	chr3:19989400-19991400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:19989600-19990400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:19989600-19990600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:19989600-19990600	Flanking Active TSS	Liver	Liver
50	chr3:19989600-19990600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links