Variant report

Variant	rs2912010
Chromosome Location	chr8:6478986-6478987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr8:6478881-6479182	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANGPT2-1	chr8:6478513-6479156	ENSG00000249898.3
2	lnc-ANGPT2-1	chr8:6478944-6479156	ENSG00000249898.3

Variant related genes	Relation type
ENSG00000271743	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1057090	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11998083	0.82[TSI][hapmap]
rs1971314	0.89[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs2911968	0.85[TSI][hapmap]
rs2912016	0.82[CEU][hapmap]
rs2912057	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs3020261	0.81[CHB][hapmap]
rs3020265	0.82[TSI][hapmap]
rs35466493	0.84[ASN][1000 genomes]
rs7017968	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs751634	0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2912010	MCPH1	cis	lymphoblastoid	seeQTL
rs2912010	LOC100132301	cis	brain	BrainEAC
rs2912010	LOC100132301	cis	temporal cortex	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6442600-6479000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr8:6457200-6479200	Weak transcription	Brain Germinal Matrix	brain
3	chr8:6457400-6479200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr8:6457800-6479200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr8:6458000-6498400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:6458600-6479800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr8:6460000-6479000	Weak transcription	Pancreas	Pancrea
8	chr8:6460200-6479000	Weak transcription	Lung	lung
9	chr8:6461400-6479800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:6464400-6479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr8:6464800-6481000	Weak transcription	Primary B cells from cord blood	blood
12	chr8:6468000-6479000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:6468600-6479200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:6469000-6479000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr8:6469000-6479000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:6469000-6479200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr8:6469000-6479400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:6469000-6479400	Weak transcription	Aorta	Aorta
19	chr8:6469000-6479400	Weak transcription	Brain Hippocampus Middle	brain
20	chr8:6470200-6479000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:6470200-6479000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr8:6471000-6479000	Weak transcription	Esophagus	oesophagus
23	chr8:6472400-6486200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:6474000-6481400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr8:6474200-6479000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr8:6474200-6479000	Weak transcription	Adipose Nuclei	Adipose
27	chr8:6474200-6479400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr8:6474200-6479400	Weak transcription	Fetal Brain Female	brain
29	chr8:6474200-6486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:6474200-6505200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr8:6474400-6479000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:6474400-6479000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr8:6474400-6479000	Weak transcription	Fetal Intestine Small	intestine
34	chr8:6474400-6479200	Weak transcription	Fetal Intestine Large	intestine
35	chr8:6474400-6479200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr8:6474400-6481400	Weak transcription	Left Ventricle	heart
37	chr8:6474600-6479000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr8:6474600-6479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr8:6474600-6479000	Weak transcription	Fetal Stomach	stomach
40	chr8:6474600-6479000	Weak transcription	Right Ventricle	heart
41	chr8:6474600-6481200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr8:6474600-6483000	Weak transcription	Fetal Lung	lung
43	chr8:6474600-6488800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr8:6474800-6479000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr8:6474800-6479200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr8:6474800-6479200	Weak transcription	NHEK	skin
47	chr8:6474800-6481400	Weak transcription	HSMMtube	muscle
48	chr8:6474800-6483600	Weak transcription	Fetal Heart	heart
49	chr8:6474800-6483600	Weak transcription	K562	blood
50	chr8:6474800-6498400	Weak transcription	HSMM	muscle

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