Variant report

Variant	rs16952372
Chromosome Location	chr15:41941796-41941797
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41939185..41941981-chr15:41952544..41954491,2	MCF-7	breast:
2	chr15:41926831..41929447-chr15:41939833..41942397,2	K562	blood:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1105881	0.92[JPT][hapmap]
rs11070343	0.93[ASN][1000 genomes]
rs1107858	0.92[JPT][hapmap]
rs11629678	0.85[ASN][1000 genomes]
rs11634956	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs12440747	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs16971976	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17676742	0.92[CHB][hapmap];0.84[JPT][hapmap]
rs17677199	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17677991	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17678138	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17678552	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs17734856	0.92[JPT][hapmap]
rs1918310	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs2241522	0.84[CHB][hapmap]
rs2303516	0.84[CHB][hapmap]
rs2303518	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2305654	0.84[JPT][hapmap]
rs28556632	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28700954	0.84[EUR][1000 genomes]
rs28810086	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28850384	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4923905	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs4924564	0.90[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924570	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs62003900	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7171123	0.80[EUR][1000 genomes]
rs8023311	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8035855	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs9672298	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9672360	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16952372	MGA	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41925000-41952200	Weak transcription	Ovary	ovary
2	chr15:41927000-41951800	Weak transcription	Hela-S3	cervix
3	chr15:41933200-41945000	Weak transcription	Right Atrium	heart
4	chr15:41939000-41942000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:41939200-41941800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr15:41939600-41941800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:41940000-41942800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:41940000-41947800	Weak transcription	Dnd41	blood
9	chr15:41940600-41942000	Weak transcription	A549	lung
10	chr15:41941000-41951400	Weak transcription	Fetal Kidney	kidney
11	chr15:41941200-41952000	Weak transcription	HSMM	muscle
12	chr15:41941400-41941800	Enhancers	NH-A	brain
13	chr15:41941600-41947200	Weak transcription	Osteobl	bone
14	chr15:41941600-41952000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:41941600-41952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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