Variant report

Variant	rs6545477
Chromosome Location	chr2:55404925-55404926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55404004..55406813-chr2:55410897..55413319,2	K562	blood:
2	chr2:55396357..55398246-chr2:55402197..55406122,3	MCF-7	breast:
3	chr2:55272935..55274858-chr2:55404512..55406306,2	K562	blood:
4	chr2:55277394..55280185-chr2:55402655..55405697,3	K562	blood:
5	chr2:55277603..55279638-chr2:55401649..55405153,3	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10167895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs10168513	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs10175803	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176835	0.91[AFR][1000 genomes]
rs10179352	0.88[AFR][1000 genomes]
rs10193886	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs10200424	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs10208867	0.90[AFR][1000 genomes]
rs1056445	0.83[YRI][hapmap]
rs11357	0.82[YRI][hapmap]
rs13395515	0.86[AFR][1000 genomes]
rs13420684	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs13427699	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1437393	0.89[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs1669	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2576711	0.86[YRI][hapmap]
rs2589092	0.83[YRI][hapmap]
rs2589096	0.86[YRI][hapmap]
rs2917779	0.86[YRI][hapmap]
rs62135101	0.82[AFR][1000 genomes]
rs67085480	1.00[ASN][1000 genomes]
rs6711753	0.89[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap]
rs6717482	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6720077	0.90[AFR][1000 genomes]
rs6727118	0.88[ASW][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6727131	0.89[ASW][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6747364	0.94[ASW][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6757361	0.87[AFR][1000 genomes]
rs9677948	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

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	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
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545477	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55386800-55416600	Weak transcription	Esophagus	oesophagus
2	chr2:55393000-55422000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:55394000-55419000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55395600-55412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55395600-55422800	Weak transcription	Ovary	ovary
6	chr2:55395600-55427000	Weak transcription	Left Ventricle	heart
7	chr2:55395800-55418200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:55395800-55418400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:55395800-55427000	Weak transcription	Aorta	Aorta
10	chr2:55396200-55407400	Weak transcription	HepG2	liver
11	chr2:55397000-55410000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:55397200-55450000	Weak transcription	NH-A	brain
13	chr2:55397400-55411600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:55397400-55422400	Weak transcription	HSMMtube	muscle
15	chr2:55397400-55423000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55399600-55419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:55399600-55423000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:55399800-55416600	Weak transcription	Primary T cells from cord blood	blood
19	chr2:55400800-55406400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:55401000-55409000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:55401600-55419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:55401800-55409000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:55402600-55422000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:55402600-55423200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
26	chr2:55403200-55408800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:55403200-55409400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:55403200-55423800	Weak transcription	Osteobl	bone
29	chr2:55403200-55426800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:55403200-55431800	Weak transcription	Fetal Brain Male	brain
31	chr2:55403400-55418800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:55403400-55423000	Weak transcription	NHEK	skin
33	chr2:55403600-55416600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:55403600-55420600	Weak transcription	HSMM	muscle
35	chr2:55404200-55423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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