Variant report

Variant	rs10846565
Chromosome Location	chr12:124352338-124352339
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124349873..124352616-chr12:124471983..124473527,2	MCF-7	breast:
2	chr12:124351615..124353844-chr12:124456020..124457584,2	MCF-7	breast:
3	chr12:124351595..124353635-chr12:124356736..124359144,2	K562	blood:
4	chr12:124344617..124346181-chr12:124350078..124352593,2	K562	blood:
5	chr12:124350568..124353635-chr12:124356736..124359633,3	K562	blood:
6	chr12:124332831..124334511-chr12:124351979..124354225,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119242	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000179195	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10773040	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10773042	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773043	0.87[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10846561	0.84[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs10846563	0.99[ASN][1000 genomes]
rs10846566	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10846567	0.82[CEU][hapmap]
rs10846568	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11057374	0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11057375	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs11057378	0.93[ASN][1000 genomes]
rs11057379	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11057380	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11057381	0.82[CEU][hapmap]
rs11057383	0.82[CEU][hapmap]
rs11057385	0.87[ASN][1000 genomes]
rs12228611	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1317312	0.82[CEU][hapmap]
rs1882488	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1882489	0.82[CEU][hapmap]
rs1922257	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1922258	0.81[CEU][hapmap]
rs7138100	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7300162	0.86[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7313897	0.82[CEU][hapmap]
rs7314963	0.93[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7959043	0.96[ASN][1000 genomes]
rs7960854	0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs7961179	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7962016	0.96[ASN][1000 genomes]
rs7980570	0.84[ASN][1000 genomes]
rs9669530	0.82[CEU][hapmap]

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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10846565	MORN3	cis	parietal	SCAN
rs10846565	CCDC92	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124331400-124352800	Weak transcription	Fetal Brain Female	brain
2	chr12:124352200-124354200	Enhancers	Fetal Brain Male	brain

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