Variant report

Variant	rs2288363
Chromosome Location	chr12:9409078-9409079
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9215605..9217908-chr12:9406280..9409151,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLRG1-3	chr12:9406532-9411248	l_599_chr12:9406531-9439851_testes

Variant related genes	Relation type
ENSG00000245105	Chromatin interaction
ENSG00000214851	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10771440	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771443	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771445	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843242	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843243	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843244	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11049800	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11049844	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579180	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581534	0.80[CEU][hapmap]
rs187536	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194037	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059760	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059761	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs252019	0.80[ASN][1000 genomes]
rs252027	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs252028	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs252029	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs252030	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs252032	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs252033	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34332	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34333	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34334	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34371	0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs34372	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs4883225	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4883226	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61916190	0.84[ASN][1000 genomes]
rs717179	0.85[ASN][1000 genomes]
rs717181	0.85[ASN][1000 genomes]
rs7299846	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7309684	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958291	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7967738	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974378	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7976100	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980226	0.85[ASN][1000 genomes]
rs7980256	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877169	0.84[CHB][hapmap]
rs968786	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	23 gene(s)	inside rSNPs	diseases
5	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
7	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
10	nsv1048917	chr12:9393282-9436132	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv898739	chr12:9398365-9435244	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2288363	DDX12P	cis	Artery Tibial	GTEx
rs2288363	RP11-22B23.1	cis	Nerve Tibial	GTEx
rs2288363	DDX12P	cis	Thyroid	GTEx
rs2288363	DDX12P	cis	Nerve Tibial	GTEx
rs2288363	RP11-22B23.1	cis	lung	GTEx
rs2288363	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2288363	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs2288363	RP11-22B23.1	cis	Whole Blood	GTEx
rs2288363	A2MP1	cis	Artery Tibial	GTEx
rs2288363	RP11-22B23.1	cis	Artery Tibial	GTEx
rs2288363	A2MP1	cis	Adipose Subcutaneous	GTEx
rs2288363	DDX12P	cis	Muscle Skeletal	GTEx
rs2288363	A2MP1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9393600-9411400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:9405600-9410000	Weak transcription	Psoas Muscle	Psoas
3	chr12:9406400-9409200	Weak transcription	HepG2	liver
4	chr12:9407600-9410000	Enhancers	Fetal Lung	lung
5	chr12:9407800-9409800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr12:9407800-9410000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:9407800-9410800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:9408200-9409200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr12:9408200-9409400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr12:9408200-9409600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:9408200-9410200	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr12:9408400-9410400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:9408600-9409200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:9408800-9409400	Enhancers	Hela-S3	cervix
15	chr12:9409000-9409400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:9409000-9409600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:9409000-9413200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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