Variant report

Variant	rs10096610
Chromosome Location	chr8:10289663-10289664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10089552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10096972	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11990519	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11991832	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12546887	0.94[ASN][1000 genomes]
rs17184083	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17788148	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4840482	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4841338	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55768320	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56169969	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56184206	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56359131	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56410018	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6987571	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6999865	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7004449	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7005230	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7005447	0.88[CEU][hapmap];0.85[YRI][hapmap]
rs7013094	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73203358	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73203359	0.85[AMR][1000 genomes]
rs73203360	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73203362	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73203376	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7460852	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10096610	MSRA	cis	cerebellum	SCAN

Chromatin state (count:27 , 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	chr8:10282600-10295200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr8:10282800-10293800	Weak transcription	Primary T cells from cord blood	blood
5	chr8:10283000-10291200	Weak transcription	Pancreas	Pancrea
6	chr8:10283200-10290800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:10283200-10291800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:10283200-10291800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr8:10283200-10293600	Weak transcription	Left Ventricle	heart
10	chr8:10283200-10294000	Weak transcription	Gastric	stomach
11	chr8:10283200-10295200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr8:10283400-10291200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:10284000-10291800	Weak transcription	Right Atrium	heart
14	chr8:10284600-10289800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:10285400-10293000	Weak transcription	Brain Angular Gyrus	brain
16	chr8:10285400-10293800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr8:10285600-10291800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:10285800-10292800	Weak transcription	Fetal Intestine Small	intestine
19	chr8:10285800-10305200	Weak transcription	Lung	lung
20	chr8:10287200-10290000	Weak transcription	Liver	Liver
21	chr8:10288000-10290600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr8:10288400-10291200	Weak transcription	Brain Germinal Matrix	brain
23	chr8:10288400-10291800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr8:10288400-10293800	Weak transcription	Fetal Brain Female	brain
25	chr8:10288800-10292200	Weak transcription	Spleen	Spleen
26	chr8:10289000-10290600	Weak transcription	Fetal Brain Male	brain
27	chr8:10289400-10289800	Strong transcription	Adipose Nuclei	Adipose

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