Variant report

Variant	rs4612650
Chromosome Location	chr1:59172792-59172793
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	chr1:59171897..59173602-chr1:59249011..59250824,2	K562	blood:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10489540	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11207278	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207284	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207297	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062727	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12070703	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12073211	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12078684	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12080369	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12082192	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12092264	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12562490	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12737926	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12742701	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1323281	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs1323282	0.84[AMR][1000 genomes]
rs17117968	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17118041	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17118097	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1961787	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2760480	0.90[TSI][hapmap]
rs2760482	0.81[CEU][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs2760483	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2760485	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2811856	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2811858	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2811865	0.82[EUR][1000 genomes]
rs2811866	0.82[EUR][1000 genomes]
rs2811867	0.83[EUR][1000 genomes]
rs2811868	0.83[EUR][1000 genomes]
rs2897558	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35180093	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244016	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4414067	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4483434	0.86[EUR][1000 genomes]
rs4553223	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4912361	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4912364	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912365	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912366	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4912371	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4912375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55677434	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55892958	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56398740	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61292499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659809	0.81[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664796	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673162	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6682078	0.89[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs999158	0.82[AMR][1000 genomes];0.87[EUR][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	esv3360957	chr1:59172638-59175090	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4612650	PCSK9	cis	parietal	SCAN
rs4612650	INADL	cis	parietal	SCAN
rs4612650	MYSM1	cis	cerebellum	SCAN
rs4612650	MYSM1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59166000-59176200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:59166200-59176200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:59166400-59186200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:59168400-59173600	Weak transcription	Fetal Brain Male	brain
5	chr1:59168600-59174200	Weak transcription	Fetal Brain Female	brain
6	chr1:59170800-59173600	Weak transcription	HepG2	liver
7	chr1:59170800-59173800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:59170800-59176400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:59171000-59173600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:59171000-59175200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:59171000-59175200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:59171000-59175400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:59171000-59175600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:59171200-59173600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:59171200-59175000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:59171200-59175400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:59171200-59175800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:59171200-59177800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links