Variant report

Variant	rs11137041
Chromosome Location	chr8:6479282-6479283
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1057090	0.85[TSI][hapmap]
rs11137038	0.84[GIH][hapmap]
rs11998083	0.93[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2011423	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2912016	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2936501	0.93[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2959798	0.93[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2959799	0.93[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs3020259	0.82[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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	17 gene(s)	inside rSNPs	diseases
6	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
12	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11137041	MCPH1	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6458000-6498400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:6458600-6479800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr8:6461400-6479800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr8:6464800-6481000	Weak transcription	Primary B cells from cord blood	blood
5	chr8:6469000-6479400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr8:6469000-6479400	Weak transcription	Aorta	Aorta
7	chr8:6469000-6479400	Weak transcription	Brain Hippocampus Middle	brain
8	chr8:6472400-6486200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:6474000-6481400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr8:6474200-6479400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr8:6474200-6479400	Weak transcription	Fetal Brain Female	brain
12	chr8:6474200-6486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:6474200-6505200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr8:6474400-6481400	Weak transcription	Left Ventricle	heart
15	chr8:6474600-6481200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr8:6474600-6483000	Weak transcription	Fetal Lung	lung
17	chr8:6474600-6488800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:6474800-6481400	Weak transcription	HSMMtube	muscle
19	chr8:6474800-6483600	Weak transcription	Fetal Heart	heart
20	chr8:6474800-6483600	Weak transcription	K562	blood
21	chr8:6474800-6498400	Weak transcription	HSMM	muscle
22	chr8:6475000-6480000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr8:6475200-6481400	Weak transcription	Right Atrium	heart
24	chr8:6475200-6482800	Weak transcription	Hela-S3	cervix
25	chr8:6476200-6484400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr8:6476400-6499000	Weak transcription	Brain Angular Gyrus	brain
27	chr8:6476400-6502800	Weak transcription	Colonic Mucosa	Colon
28	chr8:6477600-6479600	Weak transcription	HepG2	liver
29	chr8:6477600-6481400	Weak transcription	Ovary	ovary
30	chr8:6477600-6485400	Strong transcription	Dnd41	blood
31	chr8:6477800-6480200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:6477800-6483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr8:6477800-6483400	Weak transcription	Osteobl	bone
34	chr8:6478000-6479600	Strong transcription	Thymus	Thymus
35	chr8:6478000-6482800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:6478000-6487400	Weak transcription	Small Intestine	intestine
37	chr8:6478200-6480200	Strong transcription	Fetal Thymus	thymus
38	chr8:6478200-6480200	Strong transcription	GM12878-XiMat	blood
39	chr8:6478200-6484800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr8:6478200-6494600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:6478400-6480000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr8:6478400-6480200	Strong transcription	Gastric	stomach
43	chr8:6478400-6481000	Strong transcription	Primary T cells from cord blood	blood
44	chr8:6478400-6481000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr8:6478400-6484000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr8:6478400-6498400	Weak transcription	HMEC	breast
47	chr8:6478600-6480200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr8:6478800-6479400	Genic enhancers	Placenta	Placenta
49	chr8:6478800-6480400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr8:6478800-6480400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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