Variant report

Variant	rs3739391
Chromosome Location	chr8:6420534-6420535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10108504	0.86[CEU][hapmap]
rs2442509	0.86[CEU][hapmap]
rs2442528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2442532	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2442537	0.82[AFR][1000 genomes]
rs2442548	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2442553	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs2442557	0.91[JPT][hapmap]
rs2515504	0.89[ASN][1000 genomes]
rs2515514	0.93[ASW][hapmap];0.88[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2515516	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs2922845	0.86[EUR][1000 genomes]
rs3739392	0.88[CEU][hapmap]
rs921291	0.92[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3739391	MCPH1	cis	cerebellum	SCAN
rs3739391	DEFA5	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6342400-6421400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr8:6364200-6478200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:6407800-6423800	Weak transcription	Spleen	Spleen
4	chr8:6415200-6424000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:6416400-6420800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr8:6416400-6422200	Enhancers	Primary B cells from peripheral blood	blood
7	chr8:6416600-6420800	Active TSS	Right Atrium	heart
8	chr8:6416600-6421000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:6416600-6421000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:6416800-6420800	Active TSS	Right Ventricle	heart
11	chr8:6416800-6442400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr8:6417000-6421200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr8:6417200-6421200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr8:6417200-6421200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr8:6417400-6420600	Active TSS	Aorta	Aorta
16	chr8:6417400-6420800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr8:6417400-6421000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr8:6417600-6424000	Weak transcription	NHEK	skin
19	chr8:6417600-6442800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr8:6418200-6420600	Active TSS	Left Ventricle	heart
21	chr8:6418200-6420600	Active TSS	NHDF-Ad	bronchial
22	chr8:6418400-6420600	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr8:6418400-6420800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr8:6418400-6420800	Flanking Active TSS	Fetal Thymus	thymus
25	chr8:6418400-6420800	Active TSS	Ovary	ovary
26	chr8:6418600-6420600	Active TSS	Brain Hippocampus Middle	brain
27	chr8:6418600-6420800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:6418600-6422600	Enhancers	HepG2	liver
29	chr8:6418800-6420600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr8:6418800-6420800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr8:6418800-6420800	Active TSS	Brain Angular Gyrus	brain
32	chr8:6418800-6421000	Active TSS	Brain Anterior Caudate	brain
33	chr8:6418800-6421000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr8:6419000-6420600	Weak transcription	K562	blood
35	chr8:6419000-6462400	Weak transcription	GM12878-XiMat	blood
36	chr8:6419200-6420800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:6419200-6421000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:6419200-6421000	Active TSS	Fetal Kidney	kidney
39	chr8:6419400-6420600	Active TSS	Brain Cingulate Gyrus	brain
40	chr8:6419400-6420800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr8:6419400-6420800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr8:6419400-6420800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr8:6419400-6420800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr8:6419400-6420800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr8:6419400-6420800	Flanking Active TSS	Placenta	Placenta
46	chr8:6419400-6420800	Flanking Active TSS	Osteobl	bone
47	chr8:6419400-6421000	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr8:6419400-6421400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:6419600-6420800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr8:6419600-6420800	Active TSS	Rectal Smooth Muscle	rectum

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