Variant report

Variant	rs2229760
Chromosome Location	chr10:50681033-50681034
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10776575	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857497	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857504	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10857506	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10857510	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11101144	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11101155	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11591393	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12146288	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1917821	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2177819	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281792	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281793	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2377900	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3750747	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3793784	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4253038	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4253160	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4253190	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4253234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7895633	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7898545	0.82[EUR][1000 genomes]
rs9971208	0.81[ASN][1000 genomes]
rs9988727	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1051636	chr10:50675292-50732280	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2229760	ERCC6	cis	cerebellum	SCAN
rs2229760	ERCC6	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50662200-50691600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr10:50662400-50690000	Weak transcription	Stomach Mucosa	stomach
3	chr10:50662400-50693200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:50662600-50691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:50663200-50693800	Weak transcription	HepG2	liver
6	chr10:50666600-50684400	Weak transcription	NHLF	lung
7	chr10:50667800-50707400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:50668000-50713400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:50670600-50691600	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr10:50671600-50686600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:50671800-50693800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:50672000-50687200	Strong transcription	Fetal Muscle Leg	muscle
13	chr10:50672000-50691800	Strong transcription	Primary T cells from cord blood	blood
14	chr10:50672200-50691800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:50672400-50691600	Strong transcription	Ovary	ovary
16	chr10:50672600-50686800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr10:50672600-50691800	Strong transcription	Adipose Nuclei	Adipose
18	chr10:50672800-50691600	Strong transcription	HUVEC	blood vessel
19	chr10:50672800-50691800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr10:50673000-50690000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr10:50673200-50683800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:50673200-50687600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr10:50673200-50688000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:50673200-50691800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:50673400-50691600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr10:50673600-50691600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:50673600-50692800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr10:50673600-50693200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr10:50673800-50685400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:50673800-50687600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr10:50673800-50687800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr10:50674000-50687800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr10:50674000-50690000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:50674000-50691600	Strong transcription	HMEC	breast
35	chr10:50674000-50691600	Strong transcription	Osteobl	bone
36	chr10:50674200-50686600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr10:50674200-50691600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:50674200-50691600	Strong transcription	Liver	Liver
39	chr10:50674400-50682200	Strong transcription	Placenta	Placenta
40	chr10:50674400-50682600	Strong transcription	Fetal Lung	lung
41	chr10:50674400-50690400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr10:50674400-50691600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr10:50674400-50691600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr10:50674400-50691800	Strong transcription	NHEK	skin
45	chr10:50674600-50686800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:50674600-50686800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr10:50674600-50687000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr10:50674600-50687200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr10:50674600-50687200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr10:50674600-50691400	Strong transcription	Monocytes-CD14+_RO01746	blood

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