Variant report

Variant	rs2554869
Chromosome Location	chr12:51236106-51236107
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr12:51235437-51236309	PBDE	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:51236059-51236109	GM12892	blood:	n/a
2	chr12:51236059-51236109	T-47D	breast:	n/a
3	chr12:51236059-51236109	NHBE	bronchial:	n/a
4	chr12:51236059-51236109	U87	brain:	n/a
5	chr12:51236059-51236109	AG09319	gingival:	n/a
6	chr12:51236059-51236109	GM06990	blood:	n/a
7	chr12:51236059-51236109	SAEC	small airway:	n/a
8	chr12:51236059-51236109	SKMC	muscle:	n/a
9	chr12:51236059-51236109	HEEpiC	esophagus:	n/a
10	chr12:51236059-51236109	HCT-116	colon:	n/a
11	chr12:51236059-51236109	NT2-D1	testis:	n/a
12	chr12:51236059-51236109	ovcar-3	ovarian:	n/a
13	chr12:51236059-51236109	MCF-7	breast:	n/a
14	chr12:51236059-51236109	ProgFib	skin:	n/a
15	chr12:51236059-51236109	HCF	heart:	n/a
16	chr12:51236059-51236109	HEK293	kidney:	embryo
17	chr12:51236059-51236109	HIPEpiC	eye:	n/a
18	chr12:51236059-51236109	AG04450	lung:	fetal
19	chr12:51236059-51236109	SK-N-SH	brain:	n/a
20	chr12:51236059-51236109	HRPEpiC	eye:	n/a
21	chr12:51236059-51236109	MCF10A-Er-Src	breast:	n/a
22	chr12:51236059-51236109	HepG2	liver:	n/a
23	chr12:51236059-51236109	HPAEpiC	pulmonary alveolar:	n/a
24	chr12:51236059-51236109	NB4	blood:	n/a
25	chr12:51236059-51236109	Jurkat	blood:	n/a
26	chr12:51236059-51236109	H1-hESC	embryonic stem cell:	embryo
27	chr12:51236059-51236109	HNPCEpiC	eye:	n/a
28	chr12:51236059-51236109	GM19239	blood:	n/a
29	chr12:51236059-51236109	ECC-1	luminal epithelium:	n/a
30	chr12:51236059-51236109	PANC-1	pancreas:	n/a
31	chr12:51236059-51236109	AG09309	skin:	n/a
32	chr12:51236059-51236109	RPTEC	kidney:	n/a
33	chr12:51236059-51236109	HMEC	breast:	n/a
34	chr12:51236059-51236109	AoSMC	blood vessel:	n/a
35	chr12:51236059-51236109	HL-60	blood:	n/a
36	chr12:51236059-51236109	PFSK-1	brain:	n/a
37	chr12:51236059-51236109	AG10803	skin:	n/a
38	chr12:51236059-51236109	IMR90	lung:	fetal
39	chr12:51236059-51236109	CMK	blood:	n/a
40	chr12:51236059-51236109	HRE	kidney:	n/a
41	chr12:51236059-51236109	BJ	skin:	n/a
42	chr12:51236059-51236109	HAEpiC	amniotic membrane:	n/a
43	chr12:51236059-51236109	K562	blood:	n/a
44	chr12:51236059-51236109	AG04449	skin:	fetal
45	chr12:51236059-51236109	GM12891	blood:	n/a
46	chr12:51236059-51236109	HCPEpiC	choroid plexus:	n/a
47	chr12:51236059-51236109	A549	lung:	n/a
48	chr12:51236059-51236109	HUVEC	blood vessel:	n/a
49	chr12:51236059-51236109	Caco-2	colon:	n/a
50	chr12:51236059-51236109	HRCEpiC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51155993..51157542-chr12:51233838..51236379,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMPRSS12	TF binding region
RN7SL519P	TF binding region
TMPRSS12	CpG island
RN7SL519P	CpG island
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10876079	1.00[EUR][1000 genomes]
rs1096028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1096029	1.00[EUR][1000 genomes]
rs11832566	1.00[EUR][1000 genomes]
rs11833478	1.00[EUR][1000 genomes]
rs12316220	1.00[EUR][1000 genomes]
rs12321891	1.00[EUR][1000 genomes]
rs12322925	1.00[EUR][1000 genomes]
rs1464436	1.00[EUR][1000 genomes]
rs1595597	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1642998	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs17125155	1.00[MEX][hapmap]
rs1879622	1.00[EUR][1000 genomes]
rs1975351	1.00[EUR][1000 genomes]
rs2037453	1.00[EUR][1000 genomes]
rs2253376	1.00[EUR][1000 genomes]
rs2359188	1.00[EUR][1000 genomes]
rs2464125	1.00[EUR][1000 genomes]
rs2468378	1.00[EUR][1000 genomes]
rs2684895	1.00[EUR][1000 genomes]
rs2684896	1.00[EUR][1000 genomes]
rs2684897	1.00[EUR][1000 genomes]
rs2684904	1.00[EUR][1000 genomes]
rs2684905	1.00[EUR][1000 genomes]
rs2684907	1.00[EUR][1000 genomes]
rs2684909	1.00[EUR][1000 genomes]
rs2700476	1.00[EUR][1000 genomes]
rs2700477	1.00[EUR][1000 genomes]
rs2700481	1.00[EUR][1000 genomes]
rs2700483	1.00[EUR][1000 genomes]
rs2731437	1.00[EUR][1000 genomes]
rs2731438	1.00[EUR][1000 genomes]
rs2731441	1.00[EUR][1000 genomes]
rs2731444	1.00[EUR][1000 genomes]
rs2731445	1.00[EUR][1000 genomes]
rs2731446	1.00[EUR][1000 genomes]
rs2731447	1.00[EUR][1000 genomes]
rs2731448	1.00[EUR][1000 genomes]
rs4768908	1.00[EUR][1000 genomes]
rs4768910	1.00[EUR][1000 genomes]
rs4768919	1.00[EUR][1000 genomes]
rs6580762	1.00[EUR][1000 genomes]
rs7973984	1.00[EUR][1000 genomes]
rs829116	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829117	0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829119	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829121	1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829136	1.00[MEX][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs829138	1.00[EUR][1000 genomes]
rs939632	1.00[EUR][1000 genomes]
rs939634	1.00[EUR][1000 genomes]
rs9943796	1.00[MEX][hapmap];1.00[EUR][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv899078	chr12:51213433-51286750	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51228400-51236600	Weak transcription	Gastric	stomach
2	chr12:51233400-51236600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:51233600-51236400	Enhancers	Placenta	Placenta
4	chr12:51235000-51236400	Weak transcription	Esophagus	oesophagus
5	chr12:51235000-51236800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:51235200-51236200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:51235200-51236200	Enhancers	K562	blood
8	chr12:51235200-51236200	Weak transcription	NHEK	skin
9	chr12:51235200-51236400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:51235200-51236600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:51235200-51236600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:51235600-51236400	Enhancers	Fetal Muscle Leg	muscle
13	chr12:51235800-51236400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:51236000-51236200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr12:51236000-51236400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:51236000-51236400	Enhancers	Pancreas	Pancrea
17	chr12:51236000-51236400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr12:51236000-51236600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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