Variant report

Variant	rs11125559
Chromosome Location	chr2:55456896-55456897
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10176835	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10179352	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10193886	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10200424	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10208867	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13395515	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13420684	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1437390	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1437393	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2118284	0.86[JPT][hapmap]
rs62135101	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6545480	0.81[YRI][hapmap]
rs6711753	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6720077	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6727118	1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6727131	1.00[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6737227	0.80[YRI][hapmap]
rs6747364	1.00[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6757361	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9677948	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11125559	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
2	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:55451000-55457600	Weak transcription	HMEC	breast
4	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:55451000-55458000	Weak transcription	Osteobl	bone
8	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
11	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
13	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
17	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
18	chr2:55451200-55458400	Weak transcription	Fetal Kidney	kidney
19	chr2:55451200-55458400	Weak transcription	Fetal Lung	lung
20	chr2:55451400-55458400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:55451400-55458400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:55451400-55458600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:55451400-55458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:55451600-55457800	Weak transcription	Placenta	Placenta
25	chr2:55451800-55458400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:55451800-55458600	Weak transcription	Fetal Intestine Small	intestine
27	chr2:55452200-55458600	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:55452400-55458400	Weak transcription	Fetal Stomach	stomach
29	chr2:55452600-55457600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:55452600-55458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:55452600-55458400	Weak transcription	Brain Germinal Matrix	brain
32	chr2:55452800-55458400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:55453000-55457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:55453000-55458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:55453000-55458400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55453000-55458600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:55453000-55458600	Weak transcription	Lung	lung
38	chr2:55453000-55458600	Weak transcription	Pancreas	Pancrea
39	chr2:55453000-55458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:55453200-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:55455000-55458400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr2:55455000-55458400	Enhancers	HepG2	liver
43	chr2:55455400-55457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:55455400-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:55455600-55458400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:55455600-55458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:55455600-55458600	Weak transcription	Adipose Nuclei	Adipose
48	chr2:55455600-55458600	Weak transcription	Brain Substantia Nigra	brain
49	chr2:55455800-55457600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:55455800-55457600	Enhancers	Dnd41	blood

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