Variant report

Variant	rs11989640
Chromosome Location	chr8:10256054-10256055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11249992	0.80[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11249995	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11249996	0.92[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11249999	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11250001	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11250002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11779205	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11785061	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12541491	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12543645	0.96[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12547997	0.88[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12548025	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12550717	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13254942	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13264580	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17151903	0.89[CHD][hapmap]
rs17767186	0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs1986972	0.88[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2001337	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2001338	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3088186	0.85[CHB][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs34155841	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34381075	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34487437	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35060302	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35406700	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35472251	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35840352	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4240645	0.91[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4292737	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4316191	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841329	0.83[CEU][hapmap]
rs6985267	0.84[CHD][hapmap]
rs6999466	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7460436	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7831557	0.81[CEU][hapmap]
rs7840461	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs9329221	0.81[CEU][hapmap]
rs9650650	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9657538	0.84[ASN][1000 genomes]
rs9657539	0.81[CHB][hapmap];0.96[CHD][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1019701	chr8:10254709-10279269	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11989640	FLJ10661	cis	parietal	SCAN
rs11989640	DEFB136	cis	parietal	SCAN
rs11989640	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs11989640	MFHAS1	cis	cerebellum	SCAN
rs11989640	PPP1R3B	cis	cerebellum	SCAN
rs11989640	FLJ10661	cis	cerebellum	SCAN
rs11989640	CLDN23	cis	multi-tissue	Pritchard
rs11989640	C8orf13	cis	multi-tissue	Pritchard
rs11989640	AGPAT5	cis	cerebellum	SCAN
rs11989640	BLK	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10235400-10256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr8:10240400-10256800	Weak transcription	Left Ventricle	heart
4	chr8:10249000-10258200	Enhancers	Fetal Muscle Leg	muscle
5	chr8:10249000-10275200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr8:10252000-10258200	Enhancers	Fetal Muscle Trunk	muscle
7	chr8:10252400-10257200	Enhancers	HepG2	liver
8	chr8:10253800-10257800	Weak transcription	Spleen	Spleen
9	chr8:10254200-10261200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr8:10254400-10257400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:10254800-10257000	Enhancers	Liver	Liver
12	chr8:10255000-10257000	Enhancers	Brain Cingulate Gyrus	brain
13	chr8:10255200-10267800	Weak transcription	Primary T cells from cord blood	blood
14	chr8:10255400-10257000	Enhancers	Brain Anterior Caudate	brain
15	chr8:10255600-10256200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr8:10255600-10256400	Enhancers	Fetal Brain Female	brain
17	chr8:10255800-10256200	Enhancers	Right Atrium	heart
18	chr8:10255800-10256400	Enhancers	Brain Germinal Matrix	brain
19	chr8:10255800-10256600	Enhancers	Pancreas	Pancrea
20	chr8:10255800-10256600	Enhancers	HSMMtube	muscle
21	chr8:10255800-10256800	Enhancers	Fetal Heart	heart
22	chr8:10255800-10256800	Enhancers	Psoas Muscle	Psoas
23	chr8:10255800-10256800	Enhancers	Rectal Smooth Muscle	rectum
24	chr8:10255800-10256800	Enhancers	HSMM	muscle
25	chr8:10255800-10257000	Enhancers	Brain Hippocampus Middle	brain
26	chr8:10255800-10257000	Enhancers	Right Ventricle	heart
27	chr8:10255800-10257000	Enhancers	Stomach Smooth Muscle	stomach
28	chr8:10256000-10256200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr8:10256000-10256200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr8:10256000-10256600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr8:10256000-10256800	Enhancers	Adipose Nuclei	Adipose
32	chr8:10256000-10258000	Enhancers	Fetal Brain Male	brain
33	chr8:10256000-10267600	Weak transcription	Brain Angular Gyrus	brain

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