Variant report

Variant	rs12677963
Chromosome Location	chr8:130586355-130586356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:130526663..130528640-chr8:130584708..130586467,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10094039	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10098310	0.85[JPT][hapmap]
rs10103048	0.95[JPT][hapmap]
rs10107630	0.90[JPT][hapmap]
rs10505544	0.83[GIH][hapmap]
rs10956482	0.86[CHD][hapmap]
rs10956483	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10956485	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs11774794	0.86[GIH][hapmap]
rs11785889	0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12542190	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12548063	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12681229	0.86[CHB][hapmap]
rs13277237	0.90[JPT][hapmap]
rs1368700	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1433577	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1433580	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1583333	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.82[YRI][hapmap]
rs1594774	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16904119	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16904121	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs16904123	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap]
rs1865223	0.90[JPT][hapmap]
rs1946627	0.81[ASN][1000 genomes]
rs2043404	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2163952	0.95[JPT][hapmap]
rs2395906	0.95[JPT][hapmap]
rs4319050	0.98[ASN][1000 genomes]
rs4407843	0.81[JPT][hapmap]
rs4480083	0.81[JPT][hapmap]
rs57924547	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59292525	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61453473	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6470739	0.82[CHD][hapmap]
rs6470742	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6470743	0.86[CHB][hapmap]
rs6982371	0.98[ASN][1000 genomes]
rs6982553	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7000230	0.92[ASN][1000 genomes]
rs7000289	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7000320	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7000372	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7005227	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7006214	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7008811	0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7011870	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs72609887	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7831493	0.92[ASN][1000 genomes]
rs7840067	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7846327	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs9642890	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs996313	0.86[CHB][hapmap];0.80[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12677963	PHF20L1	cis	cerebellum	SCAN
rs12677963	KCNQ3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:130568800-130587000	Weak transcription	Thymus	Thymus
2	chr8:130583200-130588800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr8:130584600-130587400	Active TSS	K562	blood
4	chr8:130585000-130588000	Flanking Active TSS	Dnd41	blood
5	chr8:130586200-130587400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links