Variant report

Variant	rs12475243
Chromosome Location	chr2:10130973-10130974
allele	G/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	MAFK	chr2:10130907-10131297	IMR90	lung:	n/a	chr2:10131108-10131119
2	POLR2A	chr2:10130742-10131264	SK-N-MC	brain:	n/a	n/a
3	MAFK	chr2:10130886-10131325	Hela-S3	cervix:	n/a	chr2:10131108-10131119
4	POLR2A	chr2:10130760-10131228	SK-N-MC	brain:	n/a	n/a
5	MAFK	chr2:10130919-10131294	HepG2	liver:	n/a	chr2:10131108-10131119
6	MAFK	chr2:10130921-10131295	K562	blood:	n/a	chr2:10131108-10131119
7	FOXP2	chr2:10130810-10131181	SK-N-MC	brain:	n/a	n/a
8	MAFF	chr2:10130907-10131291	K562	blood:	n/a	n/a
9	YY1	chr2:10130843-10131140	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr2:10130874-10131299	HepG2	liver:	n/a	chr2:10131108-10131119
11	MAFF	chr2:10130869-10131308	HepG2	liver:	n/a	n/a
12	MAFK	chr2:10130796-10131570	H1-hESC	embryonic stem cell:	n/a	chr2:10131108-10131119

No.	Distal block	Cell Line	Cell type
1	chr2:10128576..10131028-chr2:10174515..10176191,2	MCF-7	breast:
2	chr2:10128526..10131575-chr2:10133695..10136149,3	K562	blood:
3	chr2:10130225..10132254-chr2:10182649..10184525,2	MCF-7	breast:

Variant related genes	Relation type
GRHL1	TF binding region
ENSG00000134317	Chromatin interaction
ENSG00000172059	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1001215	0.93[ASN][1000 genomes]
rs11893362	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12472800	0.99[ASN][1000 genomes]
rs12614084	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12616347	0.91[ASN][1000 genomes]
rs12618788	0.99[ASN][1000 genomes]
rs12623004	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1367383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1367384	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1367388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1367389	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430621	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549752	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549754	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1820964	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1835424	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1897165	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011516	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011523	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033326	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28444564	0.99[ASN][1000 genomes]
rs34950562	1.00[ASN][1000 genomes]
rs35341467	1.00[ASN][1000 genomes]
rs35646916	0.95[ASN][1000 genomes]
rs36033432	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791753	0.97[ASN][1000 genomes]
rs3791758	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791760	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4610026	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6432047	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6432048	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6743918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731453	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7596288	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs891500	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS 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	32 gene(s)	inside rSNPs	diseases
7	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers 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	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:10101600-10136400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:10102200-10136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:10113400-10136800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:10113400-10141200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:10120400-10131800	Weak transcription	Dnd41	blood
8	chr2:10124000-10136400	Weak transcription	Hela-S3	cervix
9	chr2:10124400-10139200	Weak transcription	Gastric	stomach
10	chr2:10124800-10131800	Weak transcription	Fetal Kidney	kidney
11	chr2:10124800-10143200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
13	chr2:10125000-10132600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:10125000-10134200	Weak transcription	Right Ventricle	heart
15	chr2:10125000-10140600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:10125000-10147600	Weak transcription	K562	blood
17	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
18	chr2:10125200-10134000	Weak transcription	Stomach Mucosa	stomach
19	chr2:10125200-10139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:10125200-10139200	Weak transcription	Pancreas	Pancrea
21	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:10125400-10131400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:10125600-10131800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:10125800-10132200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:10126000-10132400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:10126000-10144000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:10126200-10132000	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:10126200-10133400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:10126200-10139200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:10126400-10133400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:10126400-10133600	Weak transcription	Small Intestine	intestine
32	chr2:10126400-10141200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:10128000-10131000	Weak transcription	Fetal Intestine Small	intestine
34	chr2:10128000-10142800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:10128000-10146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:10128400-10131400	Strong transcription	Placenta	Placenta
37	chr2:10128600-10140800	Weak transcription	Fetal Brain Male	brain
38	chr2:10128800-10131800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:10128800-10133400	Weak transcription	Esophagus	oesophagus
40	chr2:10130000-10142000	Strong transcription	HepG2	liver
41	chr2:10130600-10131800	Enhancers	HUVEC	blood vessel
42	chr2:10130600-10132000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:10130600-10134200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:10130800-10131000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:10130800-10131200	Enhancers	Fetal Muscle Trunk	muscle
46	chr2:10130800-10131200	Enhancers	Lung	lung
47	chr2:10130800-10131400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:10130800-10131400	Enhancers	GM12878-XiMat	blood
49	chr2:10130800-10131600	Enhancers	Left Ventricle	heart
50	chr2:10130800-10131600	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links