Variant report

Variant	rs12917076
Chromosome Location	chr15:59523327-59523328
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	POLR2A	chr15:59523267-59523425	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:59523188-59523737	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:59523105-59523535	GM12891	blood:	n/a	n/a
4	USF2	chr15:59523246-59523659	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:59523098-59525315	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:59523213-59523522	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
MYO1E	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10775169	0.91[EUR][1000 genomes]
rs11855088	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12437559	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12437571	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12439560	0.93[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12441621	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12443328	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs12593382	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12595001	0.83[CEU][hapmap]
rs12595677	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12912088	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236495	0.94[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17236502	0.94[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17236509	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs17302240	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17302247	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2306783	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2306784	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2414624	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28368974	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34310505	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34540528	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34827755	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3794489	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794490	0.87[YRI][hapmap]
rs4074433	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4074434	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4077169	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4287498	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4420472	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4482215	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4597251	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4775137	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56752228	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6494081	0.94[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6494091	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67037466	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67599725	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68078916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68084852	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7166002	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7180541	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72625730	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72746841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030006	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8031729	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs8039095	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
2	chr15:59487800-59524400	Weak transcription	Small Intestine	intestine
3	chr15:59497000-59524800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:59500000-59524400	Weak transcription	Right Ventricle	heart
5	chr15:59500600-59524600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:59501200-59523400	Weak transcription	Ovary	ovary
7	chr15:59501200-59525600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:59502800-59525800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
10	chr15:59514800-59524200	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:59515000-59524400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:59515400-59523800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
14	chr15:59516400-59524600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:59516600-59524400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:59516600-59529400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:59517000-59524200	Strong transcription	HSMM	muscle
18	chr15:59517000-59530200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:59517000-59536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:59517200-59524400	Weak transcription	Aorta	Aorta
21	chr15:59517200-59524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:59517200-59528600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:59517200-59528800	Weak transcription	Primary B cells from cord blood	blood
24	chr15:59517200-59529000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:59517400-59523400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:59517400-59524600	Weak transcription	Fetal Heart	heart
27	chr15:59517400-59529000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:59517400-59530000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:59517600-59523400	Weak transcription	Adipose Nuclei	Adipose
30	chr15:59517600-59523800	Weak transcription	Lung	lung
31	chr15:59517600-59524600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:59517600-59525000	Weak transcription	Spleen	Spleen
33	chr15:59517600-59528600	Weak transcription	HepG2	liver
34	chr15:59517600-59529000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:59517800-59523400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:59517800-59524200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:59517800-59524600	Weak transcription	Brain Anterior Caudate	brain
39	chr15:59517800-59528600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:59518000-59528800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:59518400-59523800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:59520000-59528800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:59520200-59523400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:59520200-59525000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:59520600-59524200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:59521200-59524000	Weak transcription	HSMMtube	muscle
48	chr15:59521400-59524000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:59521600-59524000	Weak transcription	Left Ventricle	heart
50	chr15:59521600-59524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links