Variant report

Variant	rs11169115
Chromosome Location	chr12:50096727-50096728
allele	A/C
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	chr12:50096637-50097881	GM12892	blood:	n/a	n/a
2	POLR2A	chr12:50096226-50101443	GM12878	blood:	n/a	n/a
3	ZNF143	chr12:50096657-50096837	GM12878	blood:	n/a	n/a
4	NFATC1	chr12:50096551-50097867	GM12878	blood:	n/a	n/a
5	ATF2	chr12:50096511-50097080	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:50096453-50098183	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:50096717-50097991	GM12891	blood:	n/a	n/a
8	TBP	chr12:50096684-50098070	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:50096215-50098262	GM12878	blood:	n/a	n/a
10	ATF2	chr12:50096327-50097968	GM12878	blood:	n/a	n/a
11	RELA	chr12:50096518-50098048	GM12891	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
12	STAT5A	chr12:50096403-50097879	GM12878	blood:	n/a	chr12:50097241-50097253 chr12:50097488-50097512 chr12:50097486-50097500
13	PBX3	chr12:50096689-50096902	GM12878	blood:	n/a	n/a
14	RFX5	chr12:50096654-50096843	GM12878	blood:	n/a	chr12:50096799-50096812
15	POLR2A	chr12:50096279-50098500	GM12892	blood:	n/a	n/a
16	RELA	chr12:50096620-50097934	GM19099	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
17	POLR2A	chr12:50096675-50096967	GM12891	blood:	n/a	n/a
18	POLR2A	chr12:50096336-50098350	GM12892	blood:	n/a	n/a
19	EBF1	chr12:50096230-50098035	GM12878	blood:	n/a	n/a
20	FOXM1	chr12:50096619-50097896	GM12878	blood:	n/a	n/a
21	RELA	chr12:50096656-50097909	GM10847	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
22	WRNIP1	chr12:50096365-50098347	GM12878	blood:	n/a	n/a
23	MXI1	chr12:50096683-50097123	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:50096596-50098032	GM12891	blood:	n/a	n/a
25	RCOR1	chr12:50096607-50097900	GM12878	blood:	n/a	n/a
26	MTA3	chr12:50096234-50098299	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:50096388-50098091	GM12878	blood:	n/a	n/a
28	NFIC	chr12:50096569-50098087	GM12878	blood:	n/a	chr12:50097245-50097261
29	POLR2A	chr12:50096573-50097824	GM12891	blood:	n/a	n/a
30	CUX1	chr12:50096462-50098058	GM12878	blood:	n/a	n/a
31	RUNX3	chr12:50096323-50096980	GM12878	blood:	n/a	n/a
32	PML	chr12:50096168-50098000	GM12878	blood:	n/a	chr12:50096534-50096542
33	POLR2A	chr12:50096293-50101579	GM12892	blood:	n/a	n/a
34	RELA	chr12:50096502-50097954	GM18951	blood:	n/a	chr12:50097643-50097652 chr12:50097643-50097652
35	MAZ	chr12:50096626-50096933	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50096479..50103459-chr12:50133671..50138995,13	K562	blood:
2	chr12:50035243..50038149-chr12:50095334..50097229,2	MCF-7	breast:
3	chr12:50090621..50092463-chr12:50096171..50099106,4	K562	blood:
4	chr12:50046987..50048509-chr12:50096714..50099634,2	MCF-7	breast:
5	chr12:50039220..50042213-chr12:50096453..50098982,2	MCF-7	breast:
6	chr12:50080608..50083488-chr12:50095334..50097821,2	MCF-7	breast:
7	chr12:50095907..50097744-chr12:50102018..50104730,2	K562	blood:
8	chr12:50093739..50096760-chr12:50100388..50102925,3	MCF-7	breast:
9	chr12:50067389..50069514-chr12:50096557..50099355,2	MCF-7	breast:

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000257570	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10128824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169110	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169114	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169120	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297814	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300919	0.83[AFR][1000 genomes]
rs12300962	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306951	1.00[AMR][1000 genomes]
rs12310580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314036	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12317162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320895	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1317263	1.00[AMR][1000 genomes]
rs17119738	1.00[AMR][1000 genomes]
rs17123787	1.00[AMR][1000 genomes]
rs17123827	1.00[AMR][1000 genomes]
rs17123879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17123924	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9804867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9805090	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 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	chr12:50093200-50096800	Weak transcription	Small Intestine	intestine
2	chr12:50093200-50097600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:50093200-50098200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:50093200-50098600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:50093200-50098800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:50093200-50099200	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:50093200-50099600	Weak transcription	Fetal Heart	heart
8	chr12:50093200-50100200	Weak transcription	Esophagus	oesophagus
9	chr12:50093400-50096800	Weak transcription	HMEC	breast
10	chr12:50093400-50097000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:50093400-50097000	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:50093400-50097000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:50093400-50097000	Weak transcription	K562	blood
14	chr12:50093400-50097200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:50093400-50097200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:50093400-50097400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:50093400-50098600	Weak transcription	Right Ventricle	heart
18	chr12:50093400-50098800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:50093400-50099200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:50093400-50099200	Weak transcription	Colonic Mucosa	Colon
21	chr12:50093400-50099800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:50093800-50096800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:50093800-50096800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:50093800-50097000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:50093800-50097200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:50093800-50097200	Weak transcription	Liver	Liver
27	chr12:50093800-50099200	Enhancers	Primary B cells from cord blood	blood
28	chr12:50094000-50096800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:50094000-50096800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:50094000-50096800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:50094000-50097000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:50094000-50097000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:50094000-50097000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:50094800-50099400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:50095000-50097200	Enhancers	HUVEC	blood vessel
36	chr12:50095200-50097000	Enhancers	HSMMtube	muscle
37	chr12:50095200-50098200	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:50095600-50096800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr12:50095600-50097400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:50095600-50099400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:50095800-50096800	Enhancers	NH-A	brain
42	chr12:50095800-50097200	Enhancers	Primary T cells from cord blood	blood
43	chr12:50095800-50097400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:50095800-50097400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:50095800-50097600	Enhancers	Spleen	Spleen
46	chr12:50095800-50097800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:50095800-50097800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:50095800-50098000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:50095800-50098200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr12:50095800-50098800	Enhancers	Fetal Muscle Leg	muscle

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