Variant report

Variant	rs6545475
Chromosome Location	chr2:55395807-55395808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55240924..55243759-chr2:55395356..55397522,2	K562	blood:
2	chr2:55273899..55278013-chr2:55394987..55400290,7	K562	blood:
3	chr2:55241591..55242697-chr2:55395415..55396418,7	MCF-7	breast:
4	chr2:55291031..55292984-chr2:55393872..55396324,2	K562	blood:
5	chr2:55275046..55275830-chr2:55395421..55396072,2	MCF-7	breast:
6	chr2:55394216..55396855-chr2:55401149..55403821,2	K562	blood:
7	chr2:55275912..55276843-chr2:55395409..55396337,3	MCF-7	breast:
8	chr2:55241818..55242793-chr2:55395477..55396356,4	MCF-7	breast:
9	chr2:55242047..55242761-chr2:55395804..55396365,2	K562	blood:
10	chr2:55126697..55127637-chr2:55395567..55396788,4	K562	blood:
11	chr2:55275783..55278013-chr2:55394198..55397050,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10172326	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193022	0.82[ASN][1000 genomes]
rs10197309	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11125556	0.81[CHB][hapmap]
rs1133181	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1133182	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs11679663	0.89[CEU][hapmap];0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11685292	0.86[AFR][1000 genomes]
rs12470651	0.82[CHB][hapmap]
rs12621144	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs12990898	0.82[CHB][hapmap]
rs13012766	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13013134	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13019355	0.88[CEU][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13021215	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13417057	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14026	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1437391	0.83[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap]
rs2576710	0.86[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap]
rs2864818	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35026006	0.82[ASN][1000 genomes]
rs35161040	0.81[AFR][1000 genomes]
rs35890669	0.82[ASN][1000 genomes]
rs3935223	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs4420737	0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs4671241	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4671242	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs4672024	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs4672025	0.82[CHB][hapmap]
rs4672026	0.80[CEU][hapmap];0.86[ASN][1000 genomes]
rs6545474	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545478	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs6714830	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759911	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595134	0.89[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7608118	0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010438	chr2:55373562-55450144	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545475	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55389200-55397400	Enhancers	NHLF	lung
3	chr2:55389800-55396000	Enhancers	Fetal Muscle Leg	muscle
4	chr2:55391000-55397000	Enhancers	Brain Angular Gyrus	brain
5	chr2:55391200-55397000	Enhancers	NHDF-Ad	bronchial
6	chr2:55392000-55397400	Enhancers	HSMM	muscle
7	chr2:55392800-55400400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:55393000-55404000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:55393400-55396200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:55394400-55396200	Enhancers	Fetal Heart	heart
13	chr2:55394600-55396200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:55394600-55396200	Enhancers	Rectal Smooth Muscle	rectum
15	chr2:55394600-55396200	Enhancers	A549	lung
16	chr2:55394600-55396400	Enhancers	Colon Smooth Muscle	Colon
17	chr2:55394600-55396400	Enhancers	Fetal Lung	lung
18	chr2:55394600-55397000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:55394800-55396000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:55394800-55396000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:55395200-55396400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr2:55395200-55397200	Enhancers	NH-A	brain
23	chr2:55395200-55400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:55395400-55396000	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:55395400-55396800	Enhancers	Brain Anterior Caudate	brain
26	chr2:55395400-55397200	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:55395400-55397200	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:55395400-55397400	Enhancers	Brain Substantia Nigra	brain
29	chr2:55395400-55398400	Enhancers	Brain Hippocampus Middle	brain
30	chr2:55395400-55400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:55395600-55396200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:55395600-55397000	Weak transcription	Pancreas	Pancrea
33	chr2:55395600-55397400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:55395600-55397400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:55395600-55399400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:55395600-55399400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:55395600-55400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:55395600-55400600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:55395600-55400600	Weak transcription	Brain Germinal Matrix	brain
40	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:55395600-55422800	Weak transcription	Ovary	ovary
42	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
43	chr2:55395800-55396200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:55395800-55396200	Enhancers	HepG2	liver
45	chr2:55395800-55397000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:55395800-55397200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:55395800-55397200	Weak transcription	Stomach Mucosa	stomach
48	chr2:55395800-55397400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:55395800-55397400	Enhancers	HSMMtube	muscle
50	chr2:55395800-55397400	Enhancers	Osteobl	bone

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