Variant report

Variant	rs2959799
Chromosome Location	chr8:6473715-6473716
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANGPT2-7	chr8:6473125-6474719	ENSG00000271743.1

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

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

rs_ID	r²[population]
rs1057090	0.80[TSI][hapmap]
rs11137038	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs11137041	0.93[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs11998083	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013938	0.81[TSI][hapmap]
rs2912016	0.81[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2936501	0.83[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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2959798	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020259	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][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
rs2959799	MCPH1	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6364200-6478200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:6442600-6479000	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr8:6450200-6478400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr8:6457200-6479200	Weak transcription	Brain Germinal Matrix	brain
5	chr8:6457400-6479200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:6457800-6479200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:6458000-6498400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:6458600-6479800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:6460000-6473800	Weak transcription	Right Atrium	heart
10	chr8:6460000-6479000	Weak transcription	Pancreas	Pancrea
11	chr8:6460200-6479000	Weak transcription	Lung	lung
12	chr8:6461400-6479800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:6463000-6474000	Weak transcription	HSMMtube	muscle
14	chr8:6464200-6474400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr8:6464400-6478400	Weak transcription	Primary T cells from cord blood	blood
16	chr8:6464400-6478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:6464400-6479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr8:6464800-6473800	Weak transcription	Spleen	Spleen
19	chr8:6464800-6481000	Weak transcription	Primary B cells from cord blood	blood
20	chr8:6465000-6478600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr8:6467800-6477600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:6468000-6479000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr8:6468600-6479200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr8:6468800-6478800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr8:6469000-6479000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:6469000-6479000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:6469000-6479200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:6469000-6479400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:6469000-6479400	Weak transcription	Aorta	Aorta
30	chr8:6469000-6479400	Weak transcription	Brain Hippocampus Middle	brain
31	chr8:6469800-6474000	Weak transcription	Right Ventricle	heart
32	chr8:6470200-6479000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr8:6470200-6479000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr8:6470400-6474000	Weak transcription	Fetal Thymus	thymus
35	chr8:6470400-6478000	Weak transcription	Thymus	Thymus
36	chr8:6471000-6479000	Weak transcription	Esophagus	oesophagus
37	chr8:6471800-6474000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr8:6471800-6474800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr8:6472000-6474600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr8:6472200-6474200	Weak transcription	Fetal Lung	lung
41	chr8:6472400-6486200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr8:6472600-6474000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr8:6472600-6474200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr8:6472800-6474000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:6472800-6474600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr8:6472800-6474800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr8:6472800-6475200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:6472800-6477600	Weak transcription	Dnd41	blood
49	chr8:6473000-6474000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr8:6473000-6474000	Weak transcription	Fetal Kidney	kidney

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