Variant report

Variant	rs533984
Chromosome Location	chr11:94199272-94199273
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	chr11:93472910..93474648-chr11:94197238..94199366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1014666	0.81[CEU][hapmap]
rs1133572	0.87[EUR][1000 genomes]
rs2508678	0.88[CEU][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2508784	0.81[CEU][hapmap]
rs2509324	0.83[CEU][hapmap]
rs472344	0.80[CEU][hapmap]
rs473297	0.81[CEU][hapmap]
rs498999	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs499952	0.83[CHD][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs500558	0.84[CEU][hapmap]
rs518276	1.00[CEU][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs541472	0.91[CEU][hapmap];0.93[CHD][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs576948	0.84[EUR][1000 genomes]
rs601341	0.93[CHD][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6483341	0.81[CEU][hapmap]
rs675478	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs682213	0.81[CEU][hapmap]
rs684507	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795745	chr11:94144987-94227993	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv1798271	chr11:94144987-94227993	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv1797582	chr11:94182992-94227993	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	esv1800372	chr11:94182992-94227993	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs533984	RP11-685N10.1	cis	Heart Left Ventricle	GTEx
rs533984	RP11-685N10.1	cis	Nerve Tibial	GTEx
rs533984	MRE11A	cis	parietal	SCAN
rs533984	MRE11A	cis	cerebellum	SCAN
rs533984	MRE11A	cis	Esophagus Mucosa	GTEx
rs533984	MRE11A	cis	Adipose Subcutaneous	GTEx
rs533984	GPR83	cis	parietal	SCAN
rs533984	MRE11A	cis	Esophagus Muscularis	GTEx
rs533984	RP11-685N10.1	cis	Esophagus Muscularis	GTEx
rs533984	MRE11A	cis	Artery Tibial	GTEx
rs533984	MRE11A	cis	lung	GTEx
rs533984	SLC36A4	cis	parietal	SCAN
rs533984	RP11-685N10.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:94152200-94206200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:94157400-94216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:94157400-94226200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:94157600-94226400	Weak transcription	Esophagus	oesophagus
5	chr11:94162800-94216400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:94162800-94225800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:94163000-94206000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:94163000-94207200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:94163400-94221000	Weak transcription	Psoas Muscle	Psoas
10	chr11:94166600-94216400	Weak transcription	Gastric	stomach
11	chr11:94166800-94202200	Weak transcription	Stomach Mucosa	stomach
12	chr11:94167200-94206000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:94167400-94226400	Weak transcription	Small Intestine	intestine
14	chr11:94167600-94206000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:94169800-94215400	Weak transcription	Brain Angular Gyrus	brain
16	chr11:94178400-94221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:94179000-94226000	Weak transcription	Colonic Mucosa	Colon
18	chr11:94179200-94200000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:94179400-94206200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr11:94180000-94217600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:94180600-94202800	Weak transcription	Brain Anterior Caudate	brain
22	chr11:94180600-94225800	Weak transcription	Brain Substantia Nigra	brain
23	chr11:94180800-94212600	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:94180800-94215800	Weak transcription	Lung	lung
25	chr11:94181000-94226400	Weak transcription	Pancreas	Pancrea
26	chr11:94181800-94215800	Weak transcription	Fetal Intestine Small	intestine
27	chr11:94183000-94205600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:94183200-94222200	Weak transcription	HMEC	breast
29	chr11:94183600-94219800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:94183600-94225800	Weak transcription	NHLF	lung
31	chr11:94184400-94225800	Weak transcription	NHDF-Ad	bronchial
32	chr11:94186600-94199800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:94189600-94201400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:94190600-94202400	Weak transcription	Fetal Lung	lung
35	chr11:94192800-94205400	Weak transcription	HUVEC	blood vessel
36	chr11:94193400-94210800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:94193600-94203600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:94193800-94200000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:94193800-94202000	Weak transcription	HepG2	liver
40	chr11:94193800-94214400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:94194000-94217400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:94194200-94203800	Weak transcription	A549	lung
43	chr11:94194400-94200800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:94194400-94213800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:94194600-94199400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:94194600-94199400	Weak transcription	Spleen	Spleen
47	chr11:94194600-94202200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:94194600-94202200	Weak transcription	Fetal Kidney	kidney
49	chr11:94194600-94202800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:94194600-94205600	Weak transcription	NH-A	brain

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