Variant report

Variant	rs9807439
Chromosome Location	chr18:29500067-29500068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29499375..29501591-chr18:29520871..29523624,3	K562	blood:

Variant related genes	Relation type
ENSG00000263823	Chromatin interaction
ENSG00000153339	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10153421	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326219	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12327141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12709653	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957365	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957830	0.85[EUR][1000 genomes]
rs12959996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963424	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.81[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963629	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965515	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965893	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12967531	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12968487	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291238	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540496	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34011014	0.97[ASN][1000 genomes]
rs34846731	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36062390	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581778	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233820	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73954904	0.97[ASN][1000 genomes]
rs73958215	0.97[ASN][1000 genomes]
rs8084584	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8086196	0.97[ASN][1000 genomes]
rs8087104	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9675795	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1057229	chr18:29335175-29514265	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9807439	KIAA1012	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29406200-29518600	Weak transcription	Fetal Brain Male	brain
2	chr18:29417600-29515600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:29431800-29512600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr18:29432600-29507600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr18:29432600-29521400	Weak transcription	Stomach Mucosa	stomach
6	chr18:29457000-29505800	Weak transcription	Brain Angular Gyrus	brain
7	chr18:29460400-29501200	Strong transcription	Liver	Liver
8	chr18:29461600-29518600	Weak transcription	Psoas Muscle	Psoas
9	chr18:29462000-29520000	Weak transcription	Fetal Heart	heart
10	chr18:29463400-29509200	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr18:29469000-29511400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:29469600-29507000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr18:29472800-29512000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr18:29473800-29503400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr18:29474200-29510800	Weak transcription	NH-A	brain
16	chr18:29478600-29522000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr18:29479600-29518600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr18:29480600-29511600	Weak transcription	Pancreas	Pancrea
19	chr18:29480600-29519400	Weak transcription	Spleen	Spleen
20	chr18:29480800-29511200	Weak transcription	Hela-S3	cervix
21	chr18:29481400-29511600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr18:29481800-29500400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr18:29481800-29503000	Weak transcription	Colon Smooth Muscle	Colon
24	chr18:29482000-29506000	Weak transcription	A549	lung
25	chr18:29482000-29511200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr18:29482200-29511200	Weak transcription	NHLF	lung
27	chr18:29482400-29511400	Weak transcription	Brain Hippocampus Middle	brain
28	chr18:29482400-29522000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr18:29482600-29506800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr18:29482600-29521600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr18:29482800-29521600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr18:29483200-29506600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr18:29483200-29511200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr18:29484200-29502200	Weak transcription	Right Ventricle	heart
35	chr18:29484400-29509200	Weak transcription	Gastric	stomach
36	chr18:29484400-29520800	Weak transcription	Fetal Brain Female	brain
37	chr18:29484800-29500400	Weak transcription	Lung	lung
38	chr18:29484800-29521000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr18:29485400-29500200	Weak transcription	Fetal Lung	lung
40	chr18:29485400-29509400	Weak transcription	Small Intestine	intestine
41	chr18:29485600-29506000	Weak transcription	Brain Substantia Nigra	brain
42	chr18:29485600-29506800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr18:29485600-29507800	Weak transcription	Colonic Mucosa	Colon
44	chr18:29485800-29508200	Weak transcription	Brain Germinal Matrix	brain
45	chr18:29487200-29502000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr18:29487600-29506400	Weak transcription	Left Ventricle	heart
47	chr18:29487600-29508200	Weak transcription	Fetal Kidney	kidney
48	chr18:29487800-29511200	Weak transcription	HSMMtube	muscle
49	chr18:29488000-29519600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr18:29488200-29505800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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