Variant report

Variant	rs12805133
Chromosome Location	chr11:66483265-66483266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66483106..66491369-chr11:66506993..66514506,29	MCF-7	breast:
2	chr11:66474245..66476239-chr11:66481393..66484422,3	MCF-7	breast:
3	chr11:66464609..66468025-chr11:66478918..66483442,5	MCF-7	breast:
4	chr11:66481433..66483634-chr11:66788478..66791159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173898	Chromatin interaction
ENSG00000173227	Chromatin interaction
ENSG00000173715	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12417769	0.94[ASN][1000 genomes]
rs12577111	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs12804382	0.96[ASN][1000 genomes]
rs1671064	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs1791684	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs1815739	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs2276138	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs2513658	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3741363	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs474602	0.87[ASN][1000 genomes]
rs477557	0.81[ASN][1000 genomes]
rs486584	0.83[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs4930387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4930391	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs498045	0.82[CHB][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs503250	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs508443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs509556	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs535211	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs540874	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap]
rs543191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs556759	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs560556	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs569818	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs572846	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs577023	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs580910	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs594313	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs608248	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs618838	0.89[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap]
rs627330	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6591221	0.86[ASN][1000 genomes]
rs677488	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs678397	0.85[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs692892	0.88[GIH][hapmap]
rs7107944	0.81[ASN][1000 genomes]
rs8432	0.86[JPT][hapmap];0.91[MEX][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	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12805133	PRDX5	cis	cerebellum	SCAN
rs12805133	KLC2	cis	parietal	SCAN
rs12805133	CCS	cis	lymphoblastoid	seeQTL
rs12805133	CTSF	cis	cerebellum	SCAN
rs12805133	ACTN3	cis	Muscle Skeletal	GTEx
rs12805133	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs12805133	UNC93B1	cis	cerebellum	SCAN
rs12805133	GANAB	cis	parietal	SCAN
rs12805133	YIF1A	cis	parietal	SCAN
rs12805133	SYT12	cis	parietal	SCAN
rs12805133	CCS	cis	multi-tissue	Pritchard
rs12805133	CTSF	cis	parietal	SCAN
rs12805133	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs12805133	CCDC85B	cis	parietal	SCAN
rs12805133	KDM2A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66446200-66485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:66452200-66485600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr11:66453000-66483400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr11:66456400-66494600	Weak transcription	Right Atrium	heart
5	chr11:66462600-66484000	Weak transcription	Brain Substantia Nigra	brain
6	chr11:66462800-66484400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:66463000-66485000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr11:66465600-66487000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:66467400-66485200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:66468400-66484600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:66468800-66487800	Strong transcription	Fetal Brain Female	brain
12	chr11:66469600-66486800	Weak transcription	A549	lung
13	chr11:66469800-66484800	Weak transcription	HepG2	liver
14	chr11:66471600-66489200	Strong transcription	Brain Germinal Matrix	brain
15	chr11:66471800-66483400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:66471800-66483600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:66471800-66483600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr11:66471800-66485000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr11:66472000-66483400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:66472000-66483400	Strong transcription	Esophagus	oesophagus
21	chr11:66472000-66483600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:66473000-66484200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:66473000-66485600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr11:66473400-66484800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr11:66473600-66484400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:66474600-66483600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:66476000-66485000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:66477600-66483600	Strong transcription	Liver	Liver
29	chr11:66478400-66484200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:66478400-66486600	Weak transcription	Hela-S3	cervix
31	chr11:66478600-66484800	Weak transcription	Lung	lung
32	chr11:66479200-66485000	Weak transcription	Fetal Intestine Large	intestine
33	chr11:66479400-66483600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:66480400-66483400	Strong transcription	Fetal Intestine Small	intestine
35	chr11:66480800-66483400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:66481600-66487000	Weak transcription	HMEC	breast
37	chr11:66481800-66487200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:66481800-66493400	Weak transcription	Fetal Brain Male	brain
39	chr11:66482200-66484800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:66482200-66486600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:66482600-66487000	Weak transcription	Spleen	Spleen
42	chr11:66482600-66494600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr11:66482800-66484800	Weak transcription	Gastric	stomach
44	chr11:66482800-66485200	Weak transcription	Fetal Kidney	kidney
45	chr11:66482800-66485600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:66482800-66486600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:66482800-66488000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:66482800-66492600	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:66483000-66484200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:66483000-66484400	Weak transcription	NHEK	skin

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