Variant report

Variant	rs12547997
Chromosome Location	chr8:10260837-10260838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11249992	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs11249994	0.83[CHB][hapmap]
rs11249995	0.80[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs11249996	0.90[ASW][hapmap];0.80[CEU][hapmap];0.83[CHB][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11249999	0.88[CEU][hapmap];1.00[LWK][hapmap];0.82[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11250001	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11250002	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11779205	0.84[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11785061	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11989640	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]
rs12541491	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12543645	0.90[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12548025	0.91[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12550717	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13254942	0.90[ASW][hapmap];0.84[CEU][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13264580	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13272232	0.89[CHB][hapmap]
rs17767186	0.81[MEX][hapmap]
rs1986972	0.84[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes]
rs2001337	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001338	0.90[ASW][hapmap];0.88[CEU][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34155841	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34381075	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34487437	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35060302	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35406700	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35472251	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35840352	0.85[EUR][1000 genomes]
rs4240645	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4292737	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4316191	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6999466	0.80[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7460436	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9650650	0.88[AMR][1000 genomes];0.88[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12547997	FLJ10661	cis	cerebellum	SCAN
rs12547997	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs12547997	PPP1R3B	cis	cerebellum	SCAN
rs12547997	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs12547997	MFHAS1	cis	cerebellum	SCAN
rs12547997	DEFB136	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10192600-10282400	Weak transcription	Gastric	stomach
2	chr8:10249000-10275200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:10254200-10261200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr8:10255200-10267800	Weak transcription	Primary T cells from cord blood	blood
5	chr8:10256000-10267600	Weak transcription	Brain Angular Gyrus	brain
6	chr8:10256800-10266400	Weak transcription	Fetal Heart	heart
7	chr8:10257000-10267600	Weak transcription	Right Ventricle	heart
8	chr8:10257000-10274400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr8:10257600-10267000	Weak transcription	Right Atrium	heart
10	chr8:10258200-10263000	Weak transcription	Spleen	Spleen
11	chr8:10258200-10263200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:10258200-10263200	Weak transcription	Liver	Liver
13	chr8:10258200-10267800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:10258200-10274400	Weak transcription	Esophagus	oesophagus
15	chr8:10258400-10261000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr8:10258400-10263200	Weak transcription	Pancreas	Pancrea
17	chr8:10258400-10265000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr8:10258600-10262400	Weak transcription	Fetal Intestine Small	intestine
19	chr8:10259600-10263200	Enhancers	Fetal Brain Male	brain
20	chr8:10259600-10263400	Enhancers	HSMMtube	muscle
21	chr8:10259600-10263800	Enhancers	Fetal Muscle Trunk	muscle
22	chr8:10259600-10264200	Enhancers	Fetal Muscle Leg	muscle
23	chr8:10260200-10261800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr8:10260600-10261000	Enhancers	Fetal Brain Female	brain

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