Variant report

Variant	rs10843463
Chromosome Location	chr12:9496981-9496982
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9494429..9497191-chr12:9497385..9498990,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10492110	0.80[GIH][hapmap]
rs10743683	0.91[JPT][hapmap]
rs1076524	0.91[JPT][hapmap]
rs11050283	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11050312	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11609263	0.90[ASN][1000 genomes]
rs12320763	0.87[JPT][hapmap]
rs1991192	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2003608	0.87[JPT][hapmap]
rs2003610	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2003859	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3954124	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4141479	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4636721	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4883241	0.92[ASW][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4883248	0.91[JPT][hapmap]
rs7310818	0.91[JPT][hapmap]
rs741623	0.81[JPT][hapmap]
rs7958583	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs7972572	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs880369	0.87[JPT][hapmap]
rs9788250	0.82[AMR][1000 genomes];0.81[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	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
5	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
6	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
7	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
8	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
9	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
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	nsv898742	chr12:9473157-9518222	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10843463	ANO2	cis	cerebellum	SCAN
rs10843463	DCAL1	cis	multi-tissue	Pritchard
rs10843463	APOBEC1	cis	cerebellum	SCAN
rs10843463	VWF	cis	cerebellum	SCAN
rs10843463	C12orf57	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9490200-9504400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:9490800-9500000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9492400-9497000	Weak transcription	Fetal Brain Male	brain
4	chr12:9492800-9500200	Enhancers	Primary T cells from cord blood	blood
5	chr12:9493200-9502400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:9493400-9500400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:9494000-9499400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:9494000-9499400	Weak transcription	Osteobl	bone
9	chr12:9494000-9502600	Weak transcription	HSMM	muscle
10	chr12:9495000-9497800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:9495600-9497000	Enhancers	HepG2	liver
12	chr12:9495600-9497800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr12:9495600-9498600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:9495800-9497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:9495800-9498400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:9496000-9497000	Enhancers	Fetal Muscle Leg	muscle
17	chr12:9496200-9499000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:9496200-9500800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:9496400-9497000	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:9496400-9498800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:9496600-9497000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:9496600-9497400	Weak transcription	Brain Substantia Nigra	brain
23	chr12:9496600-9497600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:9496600-9497600	Weak transcription	Dnd41	blood
25	chr12:9496800-9497000	Weak transcription	Fetal Lung	lung
26	chr12:9496800-9498000	Weak transcription	Primary T cells fromperipheralblood	blood

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