Variant report

Variant	rs10881097
Chromosome Location	chr12:47763331-47763332
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47760869..47762388-chr12:47762842..47764591,2	MCF-7	breast:
2	chr12:47758575..47760381-chr12:47762018..47764513,2	K562	blood:
3	chr12:47763219..47766043-chr12:47768327..47771310,3	MCF-7	breast:
4	chr12:47763265..47765789-chr12:47773543..47775624,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10748469	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10785674	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10785676	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10881095	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10881099	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183899	0.83[EUR][1000 genomes]
rs11183919	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12302802	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1421355	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768151	0.81[ASN][1000 genomes]
rs4768152	0.83[ASN][1000 genomes]
rs4768802	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58058166	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582705	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582706	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7297927	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7956037	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7966682	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7967683	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7969338	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs886260	0.95[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs929225	0.81[ASW][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9971912	0.82[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	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10881097	SLC38A4	cis	cerebellum	SCAN
rs10881097	OR8S1	cis	cerebellum	SCAN
rs10881097	HDAC7	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47756200-47771000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:47759200-47763400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:47761200-47763400	Enhancers	Primary T cells fromperipheralblood	blood
4	chr12:47762200-47764200	Enhancers	Fetal Thymus	thymus
5	chr12:47762800-47771800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:47763000-47765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:47763200-47763400	Enhancers	Thymus	Thymus
8	chr12:47763200-47765800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:47763200-47770800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:47763200-47772200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:47763200-47772200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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