Variant report

Variant	rs12270209
Chromosome Location	chr11:57537787-57537788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10750870	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10792110	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896644	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896649	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896653	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229109	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229119	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11570176	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11570181	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12274865	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363024	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12805343	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424753	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1613592	0.84[ASN][1000 genomes]
rs1624389	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1631684	0.81[ASN][1000 genomes]
rs1647394	0.81[ASN][1000 genomes]
rs1647403	0.84[ASN][1000 genomes]
rs17455422	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455626	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783818	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783824	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783976	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783977	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1783978	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783979	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783980	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783981	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783985	0.84[ASN][1000 genomes]
rs1785498	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1785499	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1786438	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1798172	0.84[ASN][1000 genomes]
rs1798173	0.84[ASN][1000 genomes]
rs2156638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2911728	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2956981	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2956982	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3017889	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36036499	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4611222	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471398	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs547118	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56392705	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs585337	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585761	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs588612	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs592785	0.81[ASN][1000 genomes]
rs593239	0.82[ASN][1000 genomes]
rs606499	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs623541	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs627145	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs639158	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs644219	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs645145	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs652191	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs652908	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653889	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs658936	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs659165	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs665058	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs671508	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs682258	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs686489	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105506	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7115528	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7117020	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120868	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7479922	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7948571	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv327	chr11:57532641-57550746	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12270209	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs12270209	ZDHHC5	Cis_1M	lymphoblastoid	RTeQTL
rs12270209	YPEL4	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57530400-57545800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:57531400-57543200	Weak transcription	Primary B cells from cord blood	blood
3	chr11:57531800-57538200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:57531800-57539800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:57531800-57543200	Weak transcription	Thymus	Thymus
6	chr11:57532600-57538200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr11:57532800-57539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:57532800-57539800	Weak transcription	NHDF-Ad	bronchial
9	chr11:57532800-57541800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:57532800-57543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:57533000-57538000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr11:57533000-57539600	Weak transcription	HMEC	breast
13	chr11:57533000-57539800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:57533000-57539800	Weak transcription	NH-A	brain
15	chr11:57533200-57538000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:57533200-57539800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr11:57533200-57539800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:57533200-57539800	Weak transcription	HSMMtube	muscle
19	chr11:57533200-57541600	Weak transcription	Hela-S3	cervix
20	chr11:57533400-57537800	Weak transcription	Fetal Thymus	thymus
21	chr11:57533400-57540200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:57533400-57540200	Weak transcription	Spleen	Spleen
23	chr11:57533400-57543000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:57533600-57538000	Weak transcription	Pancreas	Pancrea
25	chr11:57533600-57538200	Weak transcription	Primary T cells from cord blood	blood
26	chr11:57533600-57538400	Weak transcription	Aorta	Aorta
27	chr11:57533600-57538400	Enhancers	HepG2	liver
28	chr11:57533600-57539600	Weak transcription	Placenta	Placenta
29	chr11:57533600-57540800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr11:57533600-57541200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:57533600-57541800	Weak transcription	Colonic Mucosa	Colon
32	chr11:57533800-57539800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:57533800-57539800	Weak transcription	Osteobl	bone
34	chr11:57533800-57541400	Weak transcription	Fetal Kidney	kidney
35	chr11:57534000-57542600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:57534200-57538200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr11:57534200-57538200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:57534200-57538200	Weak transcription	NHEK	skin
39	chr11:57534200-57539200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:57534200-57539600	Weak transcription	Fetal Muscle Leg	muscle
41	chr11:57534200-57539600	Weak transcription	Ovary	ovary
42	chr11:57534200-57539800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:57534200-57539800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:57534200-57539800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:57534200-57540200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:57534200-57541600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr11:57534200-57541600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:57534200-57542400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:57534200-57542600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:57534400-57539000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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