Variant report

Variant	rs2445578
Chromosome Location	chr11:86788434-86788435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:86773350..86775874-chr11:86786933..86789262,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs2001411	0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap]
rs2124581	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2244970	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2445541	0.82[CHB][hapmap]
rs2445542	0.82[CHB][hapmap]
rs2445546	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2445551	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2445557	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2445559	0.82[CHB][hapmap]
rs2445566	0.82[CHB][hapmap]
rs2445567	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2445569	0.82[CHB][hapmap]
rs2445576	0.81[JPT][hapmap]
rs2445579	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2512325	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2512327	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2512328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2512337	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2512348	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2512352	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2512353	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2512358	0.89[JPT][hapmap]
rs2512380	0.82[CHB][hapmap]
rs2512382	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2512383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2512384	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2512385	0.82[CHB][hapmap]
rs2512386	0.82[CHB][hapmap]
rs2512387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2512390	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2512485	0.85[JPT][hapmap]
rs2512488	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2512489	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2512501	0.82[CHB][hapmap]
rs2513207	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs2513222	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2513226	0.82[CHB][hapmap]
rs2513228	0.81[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs2513240	0.81[GIH][hapmap]
rs4943971	0.81[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs56686948	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv1844274	chr11:86776992-86872908	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2445578	TMEM126A	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86769200-86791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr11:86769200-86792400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:86770400-86808200	Weak transcription	HUVEC	blood vessel
4	chr11:86773000-86790800	Weak transcription	NHLF	lung
5	chr11:86773000-86792000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr11:86774600-86792400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:86774800-86806400	Weak transcription	Small Intestine	intestine
8	chr11:86775600-86791400	Weak transcription	HSMM	muscle
9	chr11:86776400-86792400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:86776600-86793000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:86776600-86815600	Weak transcription	HSMMtube	muscle
12	chr11:86777400-86792400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr11:86778400-86792400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:86778800-86789000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:86778800-86789600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:86778800-86791800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:86778800-86792400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:86779000-86790200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:86779400-86792400	Weak transcription	GM12878-XiMat	blood
20	chr11:86779600-86792200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:86780200-86788600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:86780200-86789400	Strong transcription	Adipose Nuclei	Adipose
23	chr11:86782600-86795400	Weak transcription	Fetal Heart	heart
24	chr11:86783000-86814000	Weak transcription	Hela-S3	cervix
25	chr11:86783200-86799000	Weak transcription	Psoas Muscle	Psoas
26	chr11:86784000-86792000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:86785600-86788600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:86785600-86789200	Strong transcription	Dnd41	blood
29	chr11:86786400-86791400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:86786600-86789000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr11:86786600-86789000	Genic enhancers	HepG2	liver
32	chr11:86786600-86789400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:86786800-86788600	Strong transcription	Placenta	Placenta
34	chr11:86786800-86788800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr11:86786800-86789000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:86786800-86789200	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:86786800-86789400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr11:86787000-86788600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr11:86787000-86789000	Strong transcription	K562	blood
40	chr11:86787200-86788600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr11:86787200-86791800	Weak transcription	Colonic Mucosa	Colon
42	chr11:86787200-86794200	Weak transcription	Brain Anterior Caudate	brain
43	chr11:86787200-86795400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr11:86787400-86788600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr11:86787400-86788600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:86787400-86788600	Strong transcription	A549	lung
47	chr11:86787400-86819600	Weak transcription	NH-A	brain
48	chr11:86787600-86788600	ZNF genes & repeats	Fetal Lung	lung
49	chr11:86787600-86788800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:86787600-86789200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links