Variant report

Variant	rs12514420
Chromosome Location	chr5:80612629-80612630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10041138	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10052929	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061143	0.92[CEU][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10062967	0.81[EUR][1000 genomes]
rs10072332	0.88[ASN][1000 genomes]
rs1039326	0.92[JPT][hapmap]
rs12516414	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs12519433	0.85[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs1566433	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16876403	0.89[CHB][hapmap]
rs17228569	0.81[CEU][hapmap]
rs2124888	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2270824	0.89[CHB][hapmap]
rs2277037	0.89[CHB][hapmap]
rs2406557	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756636	0.81[CEU][hapmap]
rs4502795	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703828	0.89[CHB][hapmap]
rs4704711	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4704713	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704714	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4704717	0.89[CHB][hapmap]
rs56938600	0.89[ASN][1000 genomes]
rs57266451	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6863732	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868743	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868762	0.85[CEU][hapmap]
rs6871676	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877340	0.84[ASN][1000 genomes]
rs6889795	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896441	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6896890	0.89[ASN][1000 genomes]
rs7718501	0.80[EUR][1000 genomes]
rs7731117	0.89[ASN][1000 genomes]
rs7734902	0.82[CEU][hapmap]
rs871701	0.83[JPT][hapmap]
rs955948	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12514420	ATP6AP1L	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80607000-80612800	Weak transcription	Fetal Intestine Small	intestine
2	chr5:80607200-80612800	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:80608600-80615800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:80608600-80623000	Weak transcription	Psoas Muscle	Psoas
5	chr5:80609800-80612800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:80609800-80613000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:80609800-80613400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:80609800-80613600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:80610000-80614600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr5:80610000-80618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:80610400-80613000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:80610600-80613000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:80610600-80621800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:80610800-80612800	Weak transcription	Adipose Nuclei	Adipose
15	chr5:80610800-80613000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:80610800-80613000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:80610800-80613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:80611000-80612800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:80611200-80612800	Weak transcription	Fetal Stomach	stomach
20	chr5:80611200-80612800	Weak transcription	Fetal Thymus	thymus
21	chr5:80611200-80612800	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:80611200-80613000	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:80611200-80616000	Weak transcription	Liver	Liver
24	chr5:80611400-80613000	Weak transcription	Primary B cells from cord blood	blood
25	chr5:80611400-80613200	Weak transcription	Left Ventricle	heart
26	chr5:80611400-80614400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:80611600-80613200	Weak transcription	Primary T cells from cord blood	blood
28	chr5:80611600-80623600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:80611800-80619000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:80612200-80623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:80612400-80612800	Enhancers	GM12878-XiMat	blood
32	chr5:80612400-80613000	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links