Variant report

Variant	rs62272220
Chromosome Location	chr3:160379441-160379442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160377138..160379638-chr3:160382685..160384289,2	K562	blood:
2	chr3:160378138..160380305-chr3:160382789..160386961,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10936207	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10936209	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936210	0.90[ASN][1000 genomes]
rs11709300	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11714916	0.81[ASN][1000 genomes]
rs11927913	0.90[ASN][1000 genomes]
rs12490985	0.81[AMR][1000 genomes]
rs13065289	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13095931	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317085	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403045	0.88[ASN][1000 genomes]
rs1522285	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs16831337	0.90[ASN][1000 genomes]
rs17236586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1879797	0.89[ASN][1000 genomes]
rs1980277	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2178452	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2367209	0.81[ASN][1000 genomes]
rs28544045	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28730907	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34362576	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34949451	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35308461	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35480231	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35664264	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35867836	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36118017	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3946273	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4133253	0.88[ASN][1000 genomes]
rs4679659	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679660	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4679909	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679910	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62272215	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62272216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62272217	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62272218	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62272219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773389	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773962	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6774379	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6774566	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6776873	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6777739	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779581	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6779671	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6787452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6797760	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6798462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801373	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6803670	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6806755	0.88[ASN][1000 genomes]
rs7610939	0.90[ASN][1000 genomes]
rs7632884	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv2757019	chr3:160351021-160380161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2759194	chr3:160351021-160380161	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv822308	chr3:160378594-160381820	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62272220	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160372600-160385200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:160378600-160381000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:160378800-160379600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:160378800-160379800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:160378800-160379800	Enhancers	Fetal Thymus	thymus
6	chr3:160378800-160380200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:160378800-160380400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:160379000-160379600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:160379200-160382400	Weak transcription	Hela-S3	cervix
10	chr3:160379200-160383800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:160379400-160379600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:160379400-160379600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:160379400-160379800	Enhancers	Thymus	Thymus
14	chr3:160379400-160379800	Enhancers	Dnd41	blood
15	chr3:160379400-160379800	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links