Variant report

Variant	rs1437393
Chromosome Location	chr2:55445311-55445312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55444067..55446129-chr2:55459574..55462143,2	MCF-7	breast:
2	chr2:55439611..55442665-chr2:55443845..55449055,6	K562	blood:
3	chr2:55439611..55442389-chr2:55444067..55447159,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTIF2-3	chr2:55445256-55445736	NONHSAT070767

Variant related genes	Relation type
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10168513	0.83[ASW][hapmap];0.90[YRI][hapmap]
rs10175803	0.83[AFR][1000 genomes]
rs10176835	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10179352	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10193886	1.00[CEU][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10200424	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10208867	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1056445	0.81[LWK][hapmap];0.86[YRI][hapmap]
rs11125559	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]
rs11357	0.86[YRI][hapmap]
rs13395515	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13420684	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13427699	0.82[AFR][1000 genomes]
rs1437390	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669	0.82[AFR][1000 genomes]
rs2118284	0.89[ASW][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs2576711	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs2589092	0.86[YRI][hapmap]
rs2589096	0.89[YRI][hapmap]
rs2917779	0.89[YRI][hapmap]
rs62135101	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545477	0.89[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs6711753	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6717482	0.86[YRI][hapmap]
rs6720077	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6727118	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6727131	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6747364	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6757361	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9677948	0.89[ASW][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	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
rs1437393	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55397200-55450000	Weak transcription	NH-A	brain
2	chr2:55402800-55450000	Weak transcription	NHDF-Ad	bronchial
3	chr2:55415400-55450000	Weak transcription	GM12878-XiMat	blood
4	chr2:55416800-55450000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:55417400-55450200	Weak transcription	Placenta	Placenta
6	chr2:55417800-55450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:55423800-55448000	Weak transcription	HSMM	muscle
8	chr2:55424200-55450000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:55424600-55449800	Weak transcription	Thymus	Thymus
10	chr2:55424600-55450000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:55424600-55450200	Weak transcription	Brain Germinal Matrix	brain
12	chr2:55424600-55451200	Weak transcription	HepG2	liver
13	chr2:55424800-55450200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:55425600-55449800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:55427400-55450200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:55427400-55450200	Weak transcription	Aorta	Aorta
17	chr2:55427400-55450600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55427400-55450600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:55429200-55449800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:55430000-55450400	Weak transcription	Left Ventricle	heart
21	chr2:55432000-55449800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:55432000-55451200	Weak transcription	Dnd41	blood
23	chr2:55432200-55450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:55432600-55448800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:55432800-55450000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:55432800-55450000	Weak transcription	Fetal Stomach	stomach
27	chr2:55433000-55448800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:55433000-55448800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:55433000-55449800	Weak transcription	Pancreas	Pancrea
30	chr2:55433000-55450200	Weak transcription	Ovary	ovary
31	chr2:55433400-55450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:55433600-55448200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:55433600-55448600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:55441200-55450000	Weak transcription	K562	blood
35	chr2:55441400-55450000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:55442800-55446800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:55444400-55450400	Weak transcription	Gastric	stomach
38	chr2:55444600-55449800	Weak transcription	Fetal Intestine Small	intestine
39	chr2:55445200-55448800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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