Variant report

Variant	rs759895
Chromosome Location	chr12:9518413-9518414
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	MTA3	chr12:9513806-9518741	GM12878	blood:	n/a	n/a
2	NFIC	chr12:9516412-9518439	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:9515210-9518678	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:9515459-9518442	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:9515268-9518663	GM12892	blood:	n/a	n/a
6	BCLAF1	chr12:9516321-9518443	GM12878	blood:	n/a	n/a
7	ATF2	chr12:9516298-9518464	GM12878	blood:	n/a	n/a
8	MTA3	chr12:9515491-9518616	GM12878	blood:	n/a	n/a
9	FOXM1	chr12:9516445-9518417	GM12878	blood:	n/a	n/a
10	CEBPB	chr12:9516410-9518549	GM12878	blood:	n/a	chr12:9518109-9518122 chr12:9518111-9518122
11	NFATC1	chr12:9516436-9518423	GM12878	blood:	n/a	n/a
12	NFIC	chr12:9516346-9518467	GM12878	blood:	n/a	n/a
13	RUNX3	chr12:9516335-9518524	GM12878	blood:	n/a	n/a
14	NFATC1	chr12:9516473-9518421	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:9515282-9518433	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:9515243-9518471	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:9515223-9518659	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9516871..9518767-chr12:9528942..9530878,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260423	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1863246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2003609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2011380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2216987	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2377798	0.97[AFR][1000 genomes]
rs2377799	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4883252	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7315226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7315243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs741619	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs741620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs741621	0.87[AMR][1000 genomes]
rs741622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs759893	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs759894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv3436788	chr12:9499151-9519686	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv3332298	chr12:9500121-9519487	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv2760260	chr12:9504060-9519172	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv898744	chr12:9518222-9668380	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9515400-9519200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:9515600-9518600	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:9515800-9518600	Enhancers	H9 Cell Line	embryonic stem cell
4	chr12:9515800-9520000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:9515800-9520000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:9516000-9519800	Weak transcription	Right Atrium	heart
7	chr12:9516000-9521200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:9516400-9520000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr12:9516600-9520000	Enhancers	Fetal Stomach	stomach
10	chr12:9516800-9518600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:9516800-9518600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:9516800-9520000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr12:9516800-9520400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:9516800-9520600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr12:9516800-9521600	Enhancers	Fetal Lung	lung
16	chr12:9517000-9518600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:9517200-9518600	Flanking Active TSS	GM12878-XiMat	blood
18	chr12:9517200-9519800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:9517400-9520000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr12:9517600-9518600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:9517600-9519600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr12:9517600-9520600	Weak transcription	Fetal Brain Male	brain
23	chr12:9517800-9518600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr12:9517800-9519400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:9517800-9519800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr12:9517800-9519800	Weak transcription	K562	blood
27	chr12:9517800-9520000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:9517800-9520200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr12:9518000-9518600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:9518000-9518800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:9518000-9518800	Enhancers	HepG2	liver
32	chr12:9518200-9518600	Enhancers	Osteobl	bone
33	chr12:9518200-9519200	Enhancers	HMEC	breast
34	chr12:9518400-9520800	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links