Variant report

Variant	rs4297107
Chromosome Location	chr9:86404584-86404585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10124390	0.83[CHB][hapmap]
rs10868051	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10868055	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868058	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10868077	0.82[CHB][hapmap]
rs11140240	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11792634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12349272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13285946	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1572030	0.83[CHB][hapmap]
rs1572031	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap]
rs192705	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.93[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];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[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]
rs295270	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs295288	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	0.83[CHB][hapmap]
rs296892	0.83[CHB][hapmap]
rs427314	0.92[EUR][1000 genomes]
rs4877803	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6559750	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7020920	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7026436	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs7041731	0.83[AMR][1000 genomes]
rs72749110	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7851636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7855503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs7875289	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs796001	0.83[CHB][hapmap]
rs9314723	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]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4297107	GKAP1	cis	cerebellum	SCAN
rs4297107	C9orf64	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86348400-86415400	Weak transcription	Fetal Heart	heart
2	chr9:86350000-86431600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:86350800-86407000	Weak transcription	Primary B cells from cord blood	blood
4	chr9:86352000-86411800	Weak transcription	Ovary	ovary
5	chr9:86353000-86432000	Weak transcription	Lung	lung
6	chr9:86363800-86412400	Weak transcription	HepG2	liver
7	chr9:86363800-86431200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:86364800-86412000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:86364800-86413400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:86367000-86413600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:86367400-86411800	Weak transcription	Brain Substantia Nigra	brain
12	chr9:86367600-86412000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:86373200-86411800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:86377000-86412600	Weak transcription	Brain Anterior Caudate	brain
15	chr9:86377200-86432000	Weak transcription	Gastric	stomach
16	chr9:86378400-86418400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:86380200-86431600	Weak transcription	Fetal Kidney	kidney
18	chr9:86381400-86411800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:86383600-86425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:86385400-86409200	Weak transcription	Primary T cells from cord blood	blood
21	chr9:86388200-86411400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:86389000-86431600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:86391800-86411800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:86392000-86431600	Weak transcription	Psoas Muscle	Psoas
25	chr9:86392000-86431800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:86393400-86412000	Weak transcription	Brain Angular Gyrus	brain
27	chr9:86393600-86412400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:86394400-86431600	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:86394800-86412600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:86395000-86416400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:86395600-86417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:86397000-86420000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:86397400-86412200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr9:86397400-86413400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr9:86397400-86415600	Weak transcription	Brain Germinal Matrix	brain
36	chr9:86397400-86419400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:86397400-86423400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:86399000-86431000	Weak transcription	A549	lung
39	chr9:86399400-86408800	Weak transcription	Fetal Intestine Small	intestine
40	chr9:86399400-86408800	Weak transcription	Left Ventricle	heart
41	chr9:86399400-86409600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:86399400-86411400	Weak transcription	Aorta	Aorta
43	chr9:86399400-86411800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr9:86399400-86412000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:86399400-86412200	Weak transcription	Fetal Muscle Leg	muscle
46	chr9:86399400-86412200	Weak transcription	Thymus	Thymus
47	chr9:86399400-86431000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:86399400-86431200	Weak transcription	Fetal Stomach	stomach
49	chr9:86399400-86431400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr9:86399400-86431600	Weak transcription	Right Ventricle	heart

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