Variant report

Variant	rs26531
Chromosome Location	chr5:115150525-115150526
allele	A/C
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	FOXA1	chr5:115150153-115150534	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115149403..115152060-chr5:115175796..115178394,2	MCF-7	breast:
2	chr5:115147173..115150653-chr5:115151450..115154733,4	K562	blood:

Variant related genes	Relation type
CDO1	TF binding region
ENSG00000145782	Chromatin interaction
ENSG00000129596	Chromatin interaction
ENSG00000177879	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10434761	0.97[ASN][1000 genomes]
rs1058600	0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11241337	0.81[CHD][hapmap]
rs12189155	0.88[ASN][1000 genomes]
rs12520248	0.97[ASN][1000 genomes]
rs12521324	0.90[ASN][1000 genomes]
rs13174348	0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs152368	0.87[CHD][hapmap]
rs152397	0.86[CHD][hapmap]
rs154757	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs154759	0.91[ASN][1000 genomes]
rs171809	0.87[CHD][hapmap]
rs258738	0.85[ASN][1000 genomes]
rs26529	0.92[CHD][hapmap]
rs26533	0.92[ASN][1000 genomes]
rs26534	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs26535	0.91[ASN][1000 genomes]
rs26536	0.81[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26537	0.86[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs26538	0.89[CHD][hapmap]
rs34850	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34851	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34852	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34869	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs35053218	0.94[ASN][1000 genomes]
rs35179959	0.94[ASN][1000 genomes]
rs35903246	0.92[ASN][1000 genomes]
rs3797568	0.84[CHD][hapmap]
rs3797569	0.86[CHD][hapmap]
rs3797570	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs40095	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4920892	0.85[ASN][1000 genomes]
rs57633641	0.93[ASN][1000 genomes]
rs6594906	0.93[ASN][1000 genomes]
rs6872406	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6880889	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs71581214	0.84[ASN][1000 genomes]
rs7726368	0.93[ASN][1000 genomes]

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	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs26531	ATG12	cis	cerebellum	SCAN
rs26531	CDO1	cis	Thyroid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115138400-115150800	Weak transcription	Brain Substantia Nigra	brain
2	chr5:115138400-115151000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:115146000-115150600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:115149000-115151800	Active TSS	Right Atrium	heart
5	chr5:115149200-115150800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
6	chr5:115149200-115150800	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr5:115149200-115151200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr5:115149200-115152800	Active TSS	Aorta	Aorta
9	chr5:115149400-115151000	Active TSS	Brain Angular Gyrus	brain
10	chr5:115149400-115151200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
11	chr5:115149600-115150800	Active TSS	Brain Cingulate Gyrus	brain
12	chr5:115149600-115151000	Flanking Active TSS	Fetal Brain Male	brain
13	chr5:115149600-115151000	Enhancers	Ovary	ovary
14	chr5:115149600-115151200	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr5:115149600-115151600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:115149600-115152200	Bivalent/Poised TSS	Psoas Muscle	Psoas
17	chr5:115149800-115150600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:115149800-115150600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:115149800-115151400	Active TSS	Placenta	Placenta
20	chr5:115149800-115153000	Active TSS	Liver	Liver
21	chr5:115150000-115150600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
22	chr5:115150000-115150600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr5:115150000-115150600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
24	chr5:115150000-115150800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:115150000-115150800	Active TSS	Brain Hippocampus Middle	brain
26	chr5:115150200-115150600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr5:115150200-115150600	Active TSS	Fetal Brain Female	brain
28	chr5:115150200-115151000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:115150200-115152600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:115150400-115150600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
31	chr5:115150400-115150600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr5:115150400-115150600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
33	chr5:115150400-115150600	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:115150400-115150600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr5:115150400-115150600	Bivalent/Poised TSS	NH-A	brain
36	chr5:115150400-115150800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
37	chr5:115150400-115150800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:115150400-115150800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:115150400-115150800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr5:115150400-115150800	Bivalent Enhancer	Fetal Kidney	kidney
41	chr5:115150400-115150800	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr5:115150400-115151200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:115150400-115151200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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