Variant report

Variant	rs17676742
Chromosome Location	chr15:41903048-41903049
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	chr15:41850576..41853126-chr15:41900769..41903357,2	K562	blood:
2	chr15:41900433..41903180-chr15:41911539..41913856,2	K562	blood:

Variant related genes	Relation type
ENSG00000092445	Chromatin interaction
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1105881	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs11070343	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1107858	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs11629678	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634956	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11638890	0.81[EUR][1000 genomes]
rs11639043	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16952372	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs16971976	0.93[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs17677199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17677991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17678138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17678552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17678767	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs17733613	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17734856	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs1918310	0.96[CEU][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs28526689	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28708888	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4923905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924564	1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4924570	1.00[ASW][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs4924575	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap]
rs8023311	0.86[ASN][1000 genomes]
rs8035855	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs9672298	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672360	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672671	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17676742	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs17676742	MGA	cis	lesional skin	skin_eQTL
rs17676742	RPAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links