Variant report

Variant	rs9314723
Chromosome Location	chr9:86426620-86426621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10124390	0.81[CHB][hapmap]
rs10868051	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10868055	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10868058	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10868077	0.81[CHB][hapmap]
rs10868079	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11140240	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11792634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12349272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12551039	0.82[CHB][hapmap]
rs13285946	0.83[EUR][1000 genomes]
rs1572030	0.82[CHB][hapmap]
rs1572031	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap]
rs192705	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs2065516	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs2780142	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295270	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295274	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs295275	0.81[EUR][1000 genomes]
rs295279	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295288	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs295291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs296885	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs296891	0.82[CHB][hapmap]
rs296892	0.82[CHB][hapmap]
rs427314	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4297107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4877803	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6559750	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6559754	0.82[CHB][hapmap]
rs7020920	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7021189	0.82[CHB][hapmap]
rs7026436	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs7041731	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72749110	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754144	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs7851636	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7855503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7869387	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs7875011	0.82[CHB][hapmap]
rs7875289	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs796001	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2761538	chr9:86401015-86451943	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9314723	GKAP1	cis	cerebellum	SCAN
rs9314723	C9orf64	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86350000-86431600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:86353000-86432000	Weak transcription	Lung	lung
3	chr9:86363800-86431200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr9:86377200-86432000	Weak transcription	Gastric	stomach
5	chr9:86380200-86431600	Weak transcription	Fetal Kidney	kidney
6	chr9:86389000-86431600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:86392000-86431600	Weak transcription	Psoas Muscle	Psoas
8	chr9:86392000-86431800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:86394400-86431600	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:86399000-86431000	Weak transcription	A549	lung
11	chr9:86399400-86431000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:86399400-86431200	Weak transcription	Fetal Stomach	stomach
13	chr9:86399400-86431400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:86399400-86431600	Weak transcription	Right Ventricle	heart
15	chr9:86399400-86431800	Weak transcription	Esophagus	oesophagus
16	chr9:86399400-86431800	Weak transcription	Pancreas	Pancrea
17	chr9:86402800-86431600	Weak transcription	Fetal Brain Female	brain
18	chr9:86407000-86431600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:86408200-86431200	Weak transcription	Dnd41	blood
20	chr9:86409800-86431600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:86410400-86432000	Weak transcription	Small Intestine	intestine
22	chr9:86411200-86431400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:86412200-86432000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:86412600-86431000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:86413200-86431200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:86413800-86431000	Weak transcription	Aorta	Aorta
27	chr9:86413800-86431200	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:86413800-86431600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:86413800-86431600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr9:86414000-86430400	Weak transcription	HepG2	liver
31	chr9:86414000-86431200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr9:86414200-86431000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr9:86414200-86431000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:86414200-86431000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:86414200-86431000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:86414200-86431200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:86414200-86431200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr9:86414200-86431400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:86414200-86431400	Weak transcription	Brain Anterior Caudate	brain
40	chr9:86414200-86431400	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:86414200-86431600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:86414200-86431600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:86414600-86431200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:86416200-86431000	Weak transcription	Fetal Heart	heart
45	chr9:86417800-86431800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:86418000-86431000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:86418000-86431000	Weak transcription	Fetal Intestine Small	intestine
48	chr9:86419200-86431600	Weak transcription	Fetal Intestine Large	intestine
49	chr9:86421200-86431200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:86421400-86430200	Weak transcription	Left Ventricle	heart

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