Variant report

Variant	rs11250007
Chromosome Location	chr8:10285086-10285087
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11250004	0.80[AMR][1000 genomes]
rs11250005	0.81[AMR][1000 genomes]
rs14879	0.94[ASW][hapmap];0.84[CEU][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3750311	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3750313	0.83[ASN][1000 genomes]
rs4349986	0.83[AMR][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	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
11	nsv890348	chr8:10265712-10289663	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
12	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11250007	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs11250007	CLDN23	cis	multi-tissue	Pritchard
rs11250007	MFHAS1	cis	cerebellum	SCAN
rs11250007	PSTPIP2	trans	lymphoblastoid	seeQTL
rs11250007	C8orf79	cis	parietal	SCAN
rs11250007	FLJ10661	cis	cerebellum	SCAN
rs11250007	TGM5	trans	lymphoblastoid	seeQTL
rs11250007	PPP1R3B	cis	cerebellum	SCAN
rs11250007	BLK	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10276000-10290400	Weak transcription	Fetal Intestine Large	intestine
2	chr8:10276000-10293600	Weak transcription	Brain Substantia Nigra	brain
3	chr8:10281000-10287200	Enhancers	Fetal Brain Male	brain
4	chr8:10282200-10285400	Enhancers	Brain Angular Gyrus	brain
5	chr8:10282200-10285400	Enhancers	Fetal Muscle Leg	muscle
6	chr8:10282400-10285600	Enhancers	Brain Cingulate Gyrus	brain
7	chr8:10282600-10285200	Enhancers	Brain Hippocampus Middle	brain
8	chr8:10282600-10295200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr8:10282800-10285200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr8:10282800-10285200	Weak transcription	Lung	lung
11	chr8:10282800-10293800	Weak transcription	Primary T cells from cord blood	blood
12	chr8:10283000-10285400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr8:10283000-10291200	Weak transcription	Pancreas	Pancrea
14	chr8:10283200-10285400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr8:10283200-10285600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:10283200-10287600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr8:10283200-10288600	Weak transcription	Right Ventricle	heart
18	chr8:10283200-10290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:10283200-10291800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:10283200-10291800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr8:10283200-10293600	Weak transcription	Left Ventricle	heart
22	chr8:10283200-10294000	Weak transcription	Gastric	stomach
23	chr8:10283200-10295200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr8:10283400-10288200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr8:10283400-10291200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr8:10283600-10285400	Enhancers	Fetal Stomach	stomach
27	chr8:10283800-10285200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:10283800-10285800	Strong transcription	Fetal Intestine Small	intestine
29	chr8:10283800-10287200	Strong transcription	Liver	Liver
30	chr8:10284000-10291800	Weak transcription	Right Atrium	heart
31	chr8:10284200-10289400	Weak transcription	Adipose Nuclei	Adipose
32	chr8:10284600-10285200	Enhancers	Rectal Smooth Muscle	rectum
33	chr8:10284600-10285800	Strong transcription	Spleen	Spleen
34	chr8:10284600-10289800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr8:10284800-10285400	Enhancers	Fetal Brain Female	brain
36	chr8:10284800-10285400	Enhancers	Stomach Smooth Muscle	stomach
37	chr8:10284800-10285800	Weak transcription	Brain Germinal Matrix	brain
38	chr8:10285000-10285200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr8:10285000-10285200	Enhancers	NH-A	brain
40	chr8:10285000-10285400	Weak transcription	Ovary	ovary
41	chr8:10285000-10286400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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