Variant report

Variant	rs2001411
Chromosome Location	chr11:86771583-86771584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs12419551	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12576009	0.81[CHB][hapmap]
rs1378879	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1531146	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531147	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1545600	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1963952	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs1968740	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1968742	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077594	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244970	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs2445535	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2445536	0.82[CHB][hapmap]
rs2445575	0.87[EUR][1000 genomes]
rs2445578	0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap]
rs2445580	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2445586	0.94[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2445589	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2512328	0.94[JPT][hapmap]
rs2512330	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2512332	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2512337	0.83[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap]
rs2512356	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2512357	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2512358	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2512365	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2512367	0.87[EUR][1000 genomes]
rs2512377	0.82[CHB][hapmap]
rs2512383	0.90[JPT][hapmap]
rs2512387	0.88[JPT][hapmap]
rs2512389	0.95[EUR][1000 genomes]
rs2512395	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2512396	0.94[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2512397	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2512485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2512499	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2513210	0.94[CEU][hapmap];0.91[CHB][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs2513212	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2513214	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2513215	0.87[EUR][1000 genomes]
rs2513216	0.87[EUR][1000 genomes]
rs2513218	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2513224	0.94[EUR][1000 genomes]
rs2513228	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2513233	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513235	0.82[CHB][hapmap]
rs2513237	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2513238	0.81[CHB][hapmap]
rs2513239	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513240	0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes]
rs3133317	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3133319	0.95[EUR][1000 genomes]
rs3133361	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4943971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496834	0.81[CHB][hapmap]
rs503939	0.81[CHB][hapmap]
rs521252	0.81[CHB][hapmap]
rs529564	0.81[CHB][hapmap]
rs581174	0.81[CHB][hapmap]
rs605313	0.81[CHB][hapmap]
rs676384	0.81[CHB][hapmap]
rs717723	0.82[CHB][hapmap]
rs7943307	0.81[EUR][1000 genomes]
rs7943346	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv898058	chr11:86754948-86889284	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2001411	TMEM126A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86750800-86780600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr11:86750800-86782000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:86750800-86787400	Weak transcription	A549	lung
4	chr11:86751000-86786800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:86751000-86787400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:86751200-86785600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:86751400-86786400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:86751600-86787000	Weak transcription	Aorta	Aorta
9	chr11:86755200-86779000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:86755400-86780200	Weak transcription	Adipose Nuclei	Adipose
11	chr11:86755400-86780400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr11:86756400-86782800	Weak transcription	Fetal Intestine Small	intestine
13	chr11:86756800-86772400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:86758200-86778600	Weak transcription	K562	blood
15	chr11:86758200-86780000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:86758200-86780400	Weak transcription	Fetal Muscle Leg	muscle
17	chr11:86758200-86783200	Weak transcription	Primary T cells from cord blood	blood
18	chr11:86758200-86786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:86758400-86772600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:86758400-86776000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:86758400-86778800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:86767400-86779000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:86767800-86782800	Weak transcription	Left Ventricle	heart
24	chr11:86769000-86774600	Weak transcription	HepG2	liver
25	chr11:86769000-86786400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:86769200-86774400	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:86769200-86786400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:86769200-86786800	Weak transcription	Brain Anterior Caudate	brain
29	chr11:86769200-86791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:86769200-86792400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr11:86769400-86778600	Weak transcription	Liver	Liver
32	chr11:86769600-86784800	Weak transcription	Ovary	ovary
33	chr11:86769600-86786600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:86770200-86784200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:86770400-86808200	Weak transcription	HUVEC	blood vessel
36	chr11:86771000-86786600	Weak transcription	Fetal Brain Male	brain
37	chr11:86771200-86786800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:86771400-86771800	Enhancers	Fetal Lung	lung
39	chr11:86771400-86778800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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