Variant report

Variant	rs11998591
Chromosome Location	chr8:10002754-10002755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10098474	0.82[CHB][hapmap]
rs10104911	0.83[CEU][hapmap];0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs11990610	0.86[CHB][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs11990614	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12114195	0.88[ASN][1000 genomes]
rs12115063	0.88[ASN][1000 genomes]
rs12547884	0.81[CHD][hapmap]
rs12550244	0.82[CHB][hapmap]
rs1484638	0.87[ASN][1000 genomes]
rs1484645	0.86[CHD][hapmap]
rs17149332	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs17151108	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs17151140	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs17151145	0.80[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17151147	0.80[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17151188	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[ASN][1000 genomes]
rs17151190	0.84[CHD][hapmap]
rs17151193	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1994223	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs1994224	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[YRI][hapmap];0.82[ASN][1000 genomes]
rs2046398	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs28653100	0.80[ASN][1000 genomes]
rs4294187	0.82[CHB][hapmap]
rs4840461	0.84[CEU][hapmap]
rs4840463	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs4840464	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4841280	0.91[CHB][hapmap];0.89[YRI][hapmap]
rs57105322	0.80[ASN][1000 genomes]
rs58764043	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62488697	0.81[ASN][1000 genomes]
rs62488709	0.84[ASN][1000 genomes]
rs62488714	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6601417	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs6988046	0.83[GIH][hapmap]
rs72626643	0.80[ASN][1000 genomes]
rs7843906	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs814422	0.84[CEU][hapmap]
rs9329214	0.81[CHB][hapmap];0.94[YRI][hapmap]
rs936749	0.91[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs963593	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs9644681	0.82[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv890344	chr8:9995515-10060638	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv831231	chr8:10001214-10189094	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11998591	PPP1R3B	cis	lymphoblastoid	seeQTL
rs11998591	TDH	cis	cerebellum	SCAN
rs11998591	DEFB134	cis	cerebellum	SCAN
rs11998591	FLJ10661	cis	cerebellum	SCAN
rs11998591	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9991200-10004600	Weak transcription	Esophagus	oesophagus
2	chr8:9992200-10004800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:9992200-10004800	Weak transcription	Right Ventricle	heart
4	chr8:9996400-10020200	Weak transcription	Pancreas	Pancrea
5	chr8:9996600-10004600	Weak transcription	Gastric	stomach
6	chr8:9996600-10004800	Weak transcription	Left Ventricle	heart
7	chr8:9996600-10005000	Weak transcription	Right Atrium	heart
8	chr8:9996600-10036200	Weak transcription	Primary T cells from cord blood	blood
9	chr8:9996800-10009600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr8:9997000-10010200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:10000000-10003000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:10000400-10003200	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr8:10000600-10002800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr8:10001200-10003800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:10001400-10002800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr8:10001400-10002800	Enhancers	Brain Angular Gyrus	brain
17	chr8:10001400-10004000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:10001400-10004800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr8:10001600-10003000	Enhancers	Brain Hippocampus Middle	brain
20	chr8:10001600-10005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:10001800-10002800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr8:10001800-10002800	Enhancers	Brain Anterior Caudate	brain
23	chr8:10001800-10003000	Enhancers	Brain Cingulate Gyrus	brain
24	chr8:10001800-10005800	Enhancers	Fetal Brain Male	brain
25	chr8:10002000-10002800	Enhancers	Fetal Brain Female	brain
26	chr8:10002200-10002800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr8:10002200-10002800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr8:10002200-10002800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr8:10002400-10002800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr8:10002400-10007400	Weak transcription	Brain Substantia Nigra	brain
31	chr8:10002400-10007600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr8:10002400-10009400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr8:10002600-10003400	Enhancers	Liver	Liver
34	chr8:10002600-10004800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr8:10002600-10007400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr8:10002600-10009600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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