Variant report

Variant	rs6989657
Chromosome Location	chr8:10330873-10330874
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10089552	0.82[JPT][hapmap]
rs10283145	0.82[JPT][hapmap]
rs10903328	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774221	0.82[JPT][hapmap]
rs11777364	0.92[CEU][hapmap]
rs11777976	1.00[JPT][hapmap]
rs11783478	1.00[CHB][hapmap]
rs11990519	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13252982	1.00[JPT][hapmap]
rs13254263	1.00[JPT][hapmap]
rs13267180	1.00[CHB][hapmap]
rs17151843	0.82[JPT][hapmap]
rs17709397	0.82[JPT][hapmap]
rs17765901	0.82[JPT][hapmap]
rs17767019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17788148	0.82[JPT][hapmap]
rs2001364	0.82[JPT][hapmap]
rs34259385	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34308302	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750310	1.00[JPT][hapmap]
rs3750311	1.00[JPT][hapmap]
rs4074083	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4342552	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4433149	0.82[JPT][hapmap]
rs4452832	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4582610	0.80[EUR][1000 genomes]
rs4610752	0.82[JPT][hapmap]
rs4841351	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4841352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56169969	0.81[ASN][1000 genomes]
rs56184206	0.81[ASN][1000 genomes]
rs56269910	0.88[ASN][1000 genomes]
rs56359131	0.81[ASN][1000 genomes]
rs56410018	0.81[ASN][1000 genomes]
rs58353554	0.84[ASN][1000 genomes]
rs60364191	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6601451	0.82[JPT][hapmap]
rs6993610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73203376	0.81[ASN][1000 genomes]
rs7824675	0.82[JPT][hapmap]
rs7831557	1.00[JPT][hapmap]
rs7833781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841921	0.82[JPT][hapmap]
rs9329223	0.96[CEU][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][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	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	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
6	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
7	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv890349	chr8:10294330-10355302	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1019090	chr8:10303099-10369061	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1024976	chr8:10303099-10385361	Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1030856	chr8:10303099-10439064	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv890350	chr8:10305317-10346588	Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1031580	chr8:10316170-10334279	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6989657	FLJ10661	cis	cerebellum	SCAN
rs6989657	CLDN23	cis	multi-tissue	Pritchard
rs6989657	MFHAS1	cis	cerebellum	SCAN
rs6989657	PRSS55	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10322000-10335400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr8:10326200-10336800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:10327000-10336600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr8:10328200-10331200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:10328200-10331600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr8:10328200-10335200	Weak transcription	Brain Substantia Nigra	brain
7	chr8:10328200-10338000	Strong transcription	Fetal Brain Female	brain
8	chr8:10329000-10345600	Weak transcription	Brain Hippocampus Middle	brain
9	chr8:10329200-10331800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr8:10329200-10339200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr8:10329200-10340400	Weak transcription	Brain Angular Gyrus	brain
12	chr8:10329200-10342200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr8:10329800-10332800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:10329800-10337200	Weak transcription	Left Ventricle	heart
15	chr8:10330000-10337000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr8:10330200-10335000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr8:10330200-10338000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr8:10330600-10331000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr8:10330600-10331000	Strong transcription	Brain Anterior Caudate	brain
20	chr8:10330600-10331000	Strong transcription	Gastric	stomach
21	chr8:10330600-10331000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
22	chr8:10330600-10331000	ZNF genes & repeats	Spleen	Spleen
23	chr8:10330600-10331200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr8:10330600-10331200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr8:10330600-10335400	Strong transcription	Liver	Liver
26	chr8:10330800-10331000	ZNF genes & repeats	Esophagus	oesophagus
27	chr8:10330800-10331000	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr8:10330800-10331000	Weak transcription	Ovary	ovary
29	chr8:10330800-10332200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr8:10330800-10332400	ZNF genes & repeats	Lung	lung
31	chr8:10330800-10332600	Strong transcription	Fetal Brain Male	brain
32	chr8:10330800-10332800	Strong transcription	Adipose Nuclei	Adipose
33	chr8:10330800-10334600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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