Variant report

Variant	rs12373006
Chromosome Location	chr15:55968539-55968540
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	GATA3	chr15:55968431-55968631	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
PRTG	TF binding region
ENSG00000259180	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10518817	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs10851589	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11852298	0.92[ASN][1000 genomes]
rs11854213	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12438177	0.90[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs12442771	0.85[CHB][hapmap]
rs12591246	0.86[CHB][hapmap]
rs12594642	0.87[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap]
rs12903822	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1371056	0.91[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap]
rs1438918	0.89[ASN][1000 genomes]
rs1530087	1.00[YRI][hapmap]
rs16976450	0.91[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs16976472	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814329	0.86[CHB][hapmap]
rs1986012	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2008336	0.90[CHB][hapmap]
rs2118781	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2414424	0.91[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs2414426	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2414427	0.91[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs2414431	0.81[CHB][hapmap]
rs28556884	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4377101	0.81[CHB][hapmap]
rs4392003	0.95[ASN][1000 genomes]
rs4774220	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774799	0.82[ASN][1000 genomes]
rs4774800	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4774802	0.90[CHB][hapmap]
rs572531	0.91[JPT][hapmap];0.82[MEX][hapmap]
rs62043869	0.89[ASN][1000 genomes]
rs62043871	0.81[ASN][1000 genomes]
rs6493805	0.90[ASN][1000 genomes]
rs6493809	0.85[CHB][hapmap]
rs6493814	0.85[CHB][hapmap]
rs71110312	0.82[ASN][1000 genomes]
rs715321	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7162879	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7163167	0.85[CHB][hapmap]
rs7165778	0.87[ASN][1000 genomes]
rs7166952	0.90[ASN][1000 genomes]
rs7171318	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7171522	0.89[ASN][1000 genomes]
rs7171834	0.89[ASN][1000 genomes]
rs7178379	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7182733	0.85[CHB][hapmap]
rs7359255	0.86[CHB][hapmap]
rs8025445	0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs8034113	0.91[ASN][1000 genomes]
rs8037136	0.81[CHB][hapmap]
rs9920076	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9920246	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9920262	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv457158	chr15:55930542-55982257	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv569541	chr15:55930542-55982257	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12373006	CYP19A1	cis	cerebellum	SCAN
rs12373006	PRTG	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55932600-55987000	Weak transcription	Ovary	ovary
4	chr15:55932800-55973400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:55942800-55974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:55952800-55972000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:55954000-55968600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:55954000-55971600	Weak transcription	Fetal Kidney	kidney
9	chr15:55954000-55975400	Weak transcription	HSMM	muscle
10	chr15:55954000-55977400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:55954200-55970000	Weak transcription	Fetal Intestine Large	intestine
12	chr15:55954400-55987000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:55954600-55975000	Weak transcription	A549	lung
14	chr15:55955400-55980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:55958200-55977600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:55958800-55977400	Weak transcription	Left Ventricle	heart
17	chr15:55959000-55973800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:55960400-55977600	Weak transcription	Placenta	Placenta
19	chr15:55960800-55995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:55961400-55972400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:55961400-55973000	Weak transcription	Psoas Muscle	Psoas
22	chr15:55962600-55974800	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:55963400-55980200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:55964000-55977200	Weak transcription	HUVEC	blood vessel
25	chr15:55964200-55975600	Weak transcription	Fetal Stomach	stomach
26	chr15:55964800-55968800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:55964800-55977200	Weak transcription	HepG2	liver
28	chr15:55966000-55974400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:55967600-55970600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:55967800-55969000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:55967800-55969200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr15:55968000-55969200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:55968000-55969200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr15:55968000-55969400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr15:55968000-55970800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:55968200-55969000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr15:55968200-55969000	Enhancers	Fetal Lung	lung
38	chr15:55968200-55969400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr15:55968400-55969200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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