Variant report

Variant	rs17151903
Chromosome Location	chr8:10253537-10253538
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11249993	0.81[EUR][1000 genomes]
rs11779205	0.81[CHB][hapmap]
rs11783514	0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11989029	0.87[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11989640	0.89[CHD][hapmap]
rs11997177	0.82[AMR][1000 genomes]
rs12544727	0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12548025	0.86[CHB][hapmap]
rs13254942	0.89[CHD][hapmap]
rs13273009	0.94[CHB][hapmap];0.81[LWK][hapmap]
rs17151824	0.88[GIH][hapmap]
rs17151892	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17151898	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17151899	0.93[CHB][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1986677	0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs1986972	0.96[CHD][hapmap]
rs2001365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4240645	0.82[ASN][1000 genomes]
rs6601447	0.87[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs6985267	0.81[CHD][hapmap]
rs7460436	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs7821526	0.86[AMR][1000 genomes]
rs7840461	0.87[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7842443	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9657538	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9657539	0.87[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][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	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv890347	chr8:10153082-10331636	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv527326	chr8:10199548-10320019	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription 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	18 gene(s)	inside rSNPs	diseases
7	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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
8	nsv465460	chr8:10241411-10290566	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	nsv610265	chr8:10241411-10290566	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv610266	chr8:10250758-10294330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17151903	MCPH1	cis	cerebellum	SCAN
rs17151903	DEFB134	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10224000-10255800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr8:10235400-10256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:10236200-10255800	Weak transcription	Pancreas	Pancrea
5	chr8:10236200-10255800	Weak transcription	Right Ventricle	heart
6	chr8:10240400-10256000	Weak transcription	Adipose Nuclei	Adipose
7	chr8:10240400-10256800	Weak transcription	Left Ventricle	heart
8	chr8:10242000-10255800	Weak transcription	Brain Germinal Matrix	brain
9	chr8:10248400-10255000	Weak transcription	Fetal Brain Female	brain
10	chr8:10249000-10258200	Enhancers	Fetal Muscle Leg	muscle
11	chr8:10249000-10275200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr8:10250000-10255400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr8:10251000-10253600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:10251200-10255200	Enhancers	Primary T cells from cord blood	blood
15	chr8:10252000-10258200	Enhancers	Fetal Muscle Trunk	muscle
16	chr8:10252200-10254000	Enhancers	Brain Angular Gyrus	brain
17	chr8:10252400-10253600	Enhancers	Brain Hippocampus Middle	brain
18	chr8:10252400-10253600	Enhancers	Right Atrium	heart
19	chr8:10252400-10253600	Enhancers	NHLF	lung
20	chr8:10252400-10253800	Enhancers	Fetal Brain Male	brain
21	chr8:10252400-10253800	Enhancers	HSMMtube	muscle
22	chr8:10252400-10257200	Enhancers	HepG2	liver
23	chr8:10252600-10253600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:10252600-10253600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr8:10252600-10253600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:10252600-10253600	Enhancers	NHDF-Ad	bronchial
27	chr8:10252800-10253600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr8:10252800-10253800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:10252800-10255800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr8:10253000-10253600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:10253000-10253800	Enhancers	Lung	lung
32	chr8:10253000-10255800	Weak transcription	HSMM	muscle
33	chr8:10253200-10253600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:10253200-10253600	Enhancers	Small Intestine	intestine
35	chr8:10253200-10253800	Enhancers	Liver	Liver
36	chr8:10253200-10253800	Enhancers	Brain Anterior Caudate	brain
37	chr8:10253200-10253800	Enhancers	Fetal Thymus	thymus
38	chr8:10253200-10253800	Enhancers	Spleen	Spleen
39	chr8:10253200-10254000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr8:10253400-10253800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr8:10253400-10254200	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr8:10253400-10255000	Weak transcription	Brain Cingulate Gyrus	brain

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