Variant report

Variant	rs10221457
Chromosome Location	chr19:52028950-52028951
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	chr19:52022591..52024363-chr19:52027242..52029055,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268777	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10405214	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs10407110	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10410468	0.85[ASW][hapmap]
rs10853836	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1840827	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054191	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs2168643	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs2864102	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs2864104	0.92[ASW][hapmap];0.82[CHD][hapmap];0.89[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2864105	0.84[ASN][1000 genomes]
rs2902665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801873	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4801874	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6509547	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509548	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6509551	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7250538	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs8100580	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs8101241	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs8101465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8103026	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8182477	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10221457	SIGLEC12	cis	Artery Aorta	GTEx
rs10221457	SIGLEC12	cis	Artery Tibial	GTEx
rs10221457	SIGLEC12	cis	lung	GTEx
rs10221457	ZNF347	cis	cerebellum	SCAN
rs10221457	GP6	cis	cerebellum	SCAN
rs10221457	ZNF547	cis	cerebellum	SCAN
rs10221457	SIGLEC12	cis	multi-tissue	Pritchard
rs10221457	SIGLEC12	cis	Adipose Subcutaneous	GTEx
rs10221457	SIGLEC12	cis	Whole Blood	GTEx
rs10221457	ZNF417	cis	cerebellum	SCAN
rs10221457	SIGLEC12	cis	Nerve Tibial	GTEx
rs10221457	PPP1R12C	cis	cerebellum	SCAN
rs10221457	ZNF552	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52024800-52034200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:52028200-52032400	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:52028600-52029000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:52028600-52029400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:52028800-52029000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr19:52028800-52029000	Enhancers	Fetal Muscle Trunk	muscle
7	chr19:52028800-52029200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr19:52028800-52029400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr19:52028800-52029400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:52028800-52029400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:52028800-52029600	Flanking Active TSS	Placenta	Placenta
12	chr19:52028800-52029800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr19:52028800-52031800	Enhancers	K562	blood

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