Variant report

Variant	rs14026
Chromosome Location	chr2:55404794-55404795
allele	A/G
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTIF2-3	chr2:55404738-55404917	NONHSAT070763

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10172326	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs10193022	0.81[AFR][1000 genomes]
rs1133181	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133182	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685292	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12616435	0.82[ASN][1000 genomes]
rs12621144	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012766	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013134	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13019355	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021215	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13023235	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13417057	0.82[AMR][1000 genomes]
rs1437391	0.82[CHB][hapmap];0.83[CHD][hapmap];0.93[YRI][hapmap]
rs2164714	0.82[CEU][hapmap];0.82[ASN][1000 genomes]
rs2576710	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2576724	0.81[ASN][1000 genomes]
rs2864818	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34054131	0.83[ASN][1000 genomes]
rs34564471	0.92[ASN][1000 genomes]
rs35026006	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35161040	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35890669	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762509	0.92[ASN][1000 genomes]
rs3935223	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4420737	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671241	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671242	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672024	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4672025	0.84[ASN][1000 genomes]
rs4672026	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4672027	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56095114	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs56339196	0.82[ASN][1000 genomes]
rs6545474	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs6545475	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]
rs6545478	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714830	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6715130	0.82[ASN][1000 genomes]
rs6759911	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7595134	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][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
rs14026	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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