Variant report

Variant	rs1165669
Chromosome Location	chr12:104318172-104318173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104314393..104320294-chr12:104321148..104324855,10	K562	blood:
2	chr12:104313626..104315645-chr12:104317034..104319454,2	K562	blood:
3	chr12:104304220..104306668-chr12:104315880..104318249,2	K562	blood:
4	chr12:104317968..104319875-chr12:104322035..104323737,2	MCF-7	breast:
5	chr12:104307373..104313115-chr12:104313555..104318873,5	K562	blood:
6	chr12:104308000..104311397-chr12:104314818..104318186,4	K562	blood:

Variant related genes	Relation type
ENSG00000214198	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000166598	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10735390	0.91[MEX][hapmap]
rs10778305	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1165670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165674	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815289	0.90[JPT][hapmap]
rs12822539	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1370413	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1370775	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs17034734	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1866069	0.83[MEX][hapmap]
rs1866071	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866072	0.91[MEX][hapmap]
rs1992208	0.85[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs2118312	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2255315	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2255324	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2255584	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2255791	0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2255794	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs2255795	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs2255797	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs2255807	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2438111	0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs2438112	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2576954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583282	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453308	0.90[CHB][hapmap]
rs66467677	0.99[ASN][1000 genomes]
rs73177924	0.98[ASN][1000 genomes]
rs73177926	0.98[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary heart disease	21626137	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1165669	FHL1	trans	lymphoblastoid	seeQTL
rs1165669	TCP11L2	cis	cerebellum	SCAN
rs1165669	ACTR6	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104306200-104320800	Weak transcription	Psoas Muscle	Psoas
2	chr12:104317200-104322600	Weak transcription	Aorta	Aorta
3	chr12:104317400-104322200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:104318000-104318200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:104318000-104318200	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:104318000-104318400	Flanking Active TSS	GM12878-XiMat	blood
7	chr12:104318000-104322400	Weak transcription	Brain Substantia Nigra	brain

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