Variant report

Variant	rs13410889
Chromosome Location	chr2:63087778-63087779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1022110	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11893131	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs12713469	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13418889	0.85[ASN][1000 genomes]
rs1468748	0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs17027429	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1828398	0.83[CHB][hapmap]
rs1877026	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2058567	0.86[ASN][1000 genomes]
rs2075375	0.83[CHD][hapmap]
rs2080227	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs2421816	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2430386	0.83[ASN][1000 genomes]
rs2539978	0.83[CHB][hapmap];0.95[CHD][hapmap]
rs2539982	0.98[ASN][1000 genomes]
rs2539990	0.87[ASN][1000 genomes]
rs2710637	0.95[CHD][hapmap]
rs2710639	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2710641	0.81[EUR][1000 genomes]
rs2710647	0.89[ASW][hapmap];0.93[YRI][hapmap]
rs2710651	0.87[ASN][1000 genomes]
rs360808	0.84[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs4671448	0.92[CEU][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs6545972	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6545973	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6705798	0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs6714241	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.85[ASN][1000 genomes]
rs7557501	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs7562149	0.83[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs7567923	0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs7591708	0.82[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.85[ASN][1000 genomes]
rs9789661	0.83[ASN][1000 genomes]
rs9973612	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv428041	chr2:63027947-63206574	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1006848	chr2:63061816-63631407	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	esv2756598	chr2:63085848-63491438	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13410889	WDPCP	cis	lymphoblastoid	seeQTL
rs13410889	MDH1	cis	cerebellum	SCAN
rs13410889	COMMD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63046400-63101800	Weak transcription	Brain Angular Gyrus	brain
2	chr2:63050600-63091800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:63052000-63099600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:63052200-63098200	Weak transcription	Hela-S3	cervix
5	chr2:63054600-63099800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:63054800-63091600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr2:63061200-63115200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:63061400-63102000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:63062000-63093000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:63071200-63097200	Strong transcription	HepG2	liver
11	chr2:63072600-63101800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:63073400-63093000	Weak transcription	Primary B cells from cord blood	blood
13	chr2:63073800-63091800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:63073800-63094600	Weak transcription	GM12878-XiMat	blood
15	chr2:63074800-63091400	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:63074800-63101600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:63075400-63089400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:63075600-63093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:63076400-63101800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:63079000-63092000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:63079000-63101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:63079400-63102000	Weak transcription	HSMMtube	muscle
23	chr2:63079600-63091800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:63079800-63099400	Strong transcription	Liver	Liver
25	chr2:63080000-63088800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:63080600-63092000	Weak transcription	Placenta	Placenta
27	chr2:63080600-63096600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:63081000-63091800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:63081000-63100800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:63081200-63101400	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:63081400-63092000	Weak transcription	NH-A	brain
32	chr2:63081400-63095400	Weak transcription	Psoas Muscle	Psoas
33	chr2:63081400-63101600	Weak transcription	Fetal Brain Male	brain
34	chr2:63081800-63091800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:63082000-63091600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:63082000-63092200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:63082000-63104200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:63082200-63092000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr2:63082400-63102000	Weak transcription	Aorta	Aorta
40	chr2:63082600-63091000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:63082600-63092400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:63082800-63101800	Weak transcription	Fetal Thymus	thymus
43	chr2:63082800-63102000	Weak transcription	Thymus	Thymus
44	chr2:63083200-63091200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:63083200-63092600	Weak transcription	NHEK	skin
46	chr2:63083200-63102000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:63083600-63091800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:63083600-63092000	Weak transcription	Brain Germinal Matrix	brain
49	chr2:63083600-63102000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:63083600-63102000	Weak transcription	Spleen	Spleen

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