Variant report

Variant	rs17125370
Chromosome Location	chr12:51497573-51497574
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	GATA3	chr12:51497327-51497652	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51474348..51478730-chr12:51495114..51501288,7	K562	blood:

Variant related genes	Relation type
ENSG00000244540	TF binding region
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10783412	1.00[JPT][hapmap]
rs11169717	1.00[ASN][1000 genomes]
rs11169718	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169719	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11169724	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11835513	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs12369066	0.86[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12372440	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12423207	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs150909	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs161044	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs161045	1.00[JPT][hapmap]
rs161046	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs161047	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17125212	0.86[ASW][hapmap];0.88[LWK][hapmap];0.92[YRI][hapmap]
rs17125227	0.93[YRI][hapmap]
rs17125245	0.93[YRI][hapmap]
rs17125367	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125416	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17125418	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17125428	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17229232	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs2029147	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2046498	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs224566	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs224569	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs224570	1.00[JPT][hapmap]
rs224573	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs224574	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2630362	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs319938	0.89[GIH][hapmap];0.86[TSI][hapmap]
rs364627	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs390424	0.82[CEU][hapmap]
rs394384	0.82[CEU][hapmap]
rs445520	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4768873	0.88[AFR][1000 genomes]
rs4768959	1.00[JPT][hapmap]
rs4768973	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs57768942	0.85[AFR][1000 genomes]
rs58022723	0.88[AFR][1000 genomes]
rs58309379	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59372312	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580779	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6580780	0.82[CEU][hapmap]
rs6580783	1.00[JPT][hapmap]
rs6580794	0.88[AFR][1000 genomes]
rs706803	0.94[GIH][hapmap];0.86[TSI][hapmap]
rs706804	1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7137990	0.96[AFR][1000 genomes]
rs7303962	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7309789	0.82[AFR][1000 genomes]
rs73305715	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73305721	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73305734	1.00[ASN][1000 genomes]
rs73305742	0.88[AFR][1000 genomes]
rs73305754	0.88[AFR][1000 genomes]
rs73305773	0.85[AFR][1000 genomes]
rs7960097	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs7968372	0.84[EUR][1000 genomes]
rs7971712	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs7972608	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7974923	1.00[JPT][hapmap]
rs7975628	1.00[JPT][hapmap]
rs7977993	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs829021	1.00[GIH][hapmap];0.93[TSI][hapmap]

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	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51499600	Weak transcription	NHLF	lung
3	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
5	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:51482800-51498000	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:51482800-51499400	Strong transcription	Fetal Stomach	stomach
8	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:51485000-51498400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:51485600-51498200	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:51485600-51498200	Strong transcription	Fetal Thymus	thymus
18	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:51486800-51497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr12:51487000-51498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:51487200-51498000	Strong transcription	Osteobl	bone
30	chr12:51487200-51498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:51487200-51498400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:51487400-51498200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:51487400-51511000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:51487600-51498000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:51487600-51498000	Strong transcription	Primary T cells from cord blood	blood
41	chr12:51487600-51498000	Strong transcription	Brain Anterior Caudate	brain
42	chr12:51487600-51498200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:51487600-51498400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:51487600-51498400	Strong transcription	Placenta	Placenta
45	chr12:51487600-51504800	Strong transcription	Adipose Nuclei	Adipose
46	chr12:51487600-51508200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr12:51487600-51512000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:51487800-51497600	Strong transcription	Brain Germinal Matrix	brain
49	chr12:51487800-51498000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:51487800-51498000	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links