Variant report

Variant	rs11050605
Chromosome Location	chr12:9534666-9534667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9532106..9535030-chr12:9800116..9802366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10843459	0.89[ASN][1000 genomes]
rs10843579	0.90[ASN][1000 genomes]
rs10843607	0.90[ASN][1000 genomes]
rs11050246	0.89[ASN][1000 genomes]
rs11050303	0.89[ASN][1000 genomes]
rs11050304	0.89[ASN][1000 genomes]
rs11050310	0.89[ASN][1000 genomes]
rs11050397	1.00[ASN][1000 genomes]
rs11050527	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050586	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050592	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050604	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370449	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370767	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12372791	1.00[ASN][1000 genomes]
rs17804845	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17804911	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113904	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194829	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34591612	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36132622	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268554	0.90[ASN][1000 genomes]
rs4548677	0.90[ASN][1000 genomes]
rs4883242	0.89[ASN][1000 genomes]
rs55635549	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55693818	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56014159	0.89[ASN][1000 genomes]
rs56236944	0.89[ASN][1000 genomes]
rs56366134	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59555818	0.81[AFR][1000 genomes]
rs7295431	0.89[ASN][1000 genomes]
rs7302181	0.89[ASN][1000 genomes]
rs73047561	0.89[ASN][1000 genomes]
rs7310088	0.90[ASN][1000 genomes]
rs7486338	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
4	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
5	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
6	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
7	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
8	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
9	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv898744	chr12:9518222-9668380	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1049903	chr12:9521487-9546454	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv898745	chr12:9529015-9716126	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	esv3323838	chr12:9531385-9535583	Enhancers Weak transcription Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11050605	LOC728715///OVOS2	Cis_chr	lymphoblastoid	RTeQTL
rs11050605	RP11-75L1.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11050605	CLEC2D	cis	Adipose Subcutaneous	GTEx
rs11050605	DDX11///DDX12///LOC642846	Cis_chr	lymphoblastoid	RTeQTL
rs11050605	CLEC2D	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9531600-9534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:9533200-9535000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:9533400-9535000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr12:9533400-9535000	Enhancers	HepG2	liver
5	chr12:9533600-9548800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:9533800-9534800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:9533800-9534800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr12:9533800-9535200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:9534000-9540000	Weak transcription	Fetal Lung	lung
10	chr12:9534400-9534800	Enhancers	Primary T cells from cord blood	blood
11	chr12:9534400-9534800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr12:9534400-9540200	Weak transcription	Spleen	Spleen
13	chr12:9534600-9535000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:9534600-9539800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:9534600-9540400	Weak transcription	Adipose Nuclei	Adipose

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