Variant report

Variant	rs71478668
Chromosome Location	chr15:58766511-58766512
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	RELA	chr15:58764999-58766778	GM12891	blood:	n/a	n/a
2	TCF12	chr15:58765024-58766553	ECC-1	luminal epithelium:	n/a	chr15:58765226-58765236
3	MAX	chr15:58764874-58766515	A549	lung:	n/a	chr15:58766177-58766186 chr15:58766176-58766185
4	RELA	chr15:58765043-58766523	GM10847	blood:	n/a	n/a
5	EBF1	chr15:58765508-58766522	GM12878	blood:	n/a	chr15:58766325-58766336
6	EP300	chr15:58764916-58766518	ECC-1	luminal epithelium:	n/a	chr15:58766176-58766185 chr15:58766177-58766186

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58623181..58625459-chr15:58764481..58766715,2	MCF-7	breast:

Variant related genes	Relation type
ALDH1A2	TF binding region
ENSG00000128918	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10518978	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634902	0.94[ASN][1000 genomes]
rs12591216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12591624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12592407	0.92[ASN][1000 genomes]
rs12593736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12593880	0.90[ASN][1000 genomes]
rs12594222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595191	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900891	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902119	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12903955	0.87[ASN][1000 genomes]
rs12904507	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906459	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12908427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910028	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16940338	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17190580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17190587	0.94[ASN][1000 genomes]
rs2414581	0.92[ASN][1000 genomes]
rs28478642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28713618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2899630	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34053638	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34225834	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34297592	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34570549	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34577128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34744603	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35633916	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35732576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35771822	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35795657	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775053	0.94[ASN][1000 genomes]
rs6494009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71478667	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71478670	0.87[ASN][1000 genomes]
rs71478671	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71478672	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162384	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162603	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7165752	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7169744	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7172556	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174539	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8029837	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8041525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58743800-58770400	Enhancers	Fetal Thymus	thymus
2	chr15:58759400-58768400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:58759400-58770400	Enhancers	Placenta	Placenta
4	chr15:58760400-58770200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:58760600-58767000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:58761000-58767200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:58761400-58766600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:58762600-58766600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr15:58763000-58769400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:58763800-58766600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:58764000-58770200	Enhancers	Fetal Muscle Leg	muscle
12	chr15:58764000-58770200	Enhancers	Thymus	Thymus
13	chr15:58764600-58767000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr15:58764600-58769600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:58764600-58769600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr15:58764600-58770200	Enhancers	Spleen	Spleen
17	chr15:58764800-58766600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:58764800-58766600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:58764800-58769600	Enhancers	HSMMtube	muscle
20	chr15:58765000-58766600	Enhancers	HSMM	muscle
21	chr15:58765000-58767600	Enhancers	HepG2	liver
22	chr15:58765000-58767800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:58765000-58768200	Enhancers	Lung	lung
24	chr15:58765000-58768400	Enhancers	Stomach Mucosa	stomach
25	chr15:58765000-58769400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:58765000-58769400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:58765000-58769600	Enhancers	Duodenum Mucosa	Duodenum
28	chr15:58765000-58769600	Enhancers	Right Atrium	heart
29	chr15:58765000-58769800	Enhancers	Adipose Nuclei	Adipose
30	chr15:58765000-58769800	Enhancers	Pancreas	Pancrea
31	chr15:58765000-58770000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr15:58765000-58770400	Enhancers	Primary hematopoietic stem cells	blood
33	chr15:58765000-58770600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:58765000-58770600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:58765400-58766800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:58765400-58767000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:58765400-58767200	Weak transcription	Brain Hippocampus Middle	brain
38	chr15:58765400-58767400	Weak transcription	Fetal Brain Male	brain
39	chr15:58765400-58769000	Weak transcription	Psoas Muscle	Psoas
40	chr15:58765400-58769200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:58765600-58766600	Weak transcription	Primary B cells from cord blood	blood
42	chr15:58765600-58766800	Weak transcription	Right Ventricle	heart
43	chr15:58765600-58766800	Enhancers	Small Intestine	intestine
44	chr15:58765600-58767000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:58765600-58767200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:58765600-58768200	Weak transcription	Fetal Stomach	stomach
47	chr15:58765600-58768800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:58765600-58769000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:58765600-58770400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:58765800-58766800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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