Variant report

Variant	rs12959996
Chromosome Location	chr18:29413405-29413406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:29412962-29413685	K562	blood:	n/a	n/a

Variant related genes	Relation type
TRAPPC8	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10153421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326219	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12326244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[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];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12709653	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957365	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957830	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12963424	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963629	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965515	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12965893	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12967531	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12968487	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291238	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540496	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34011014	0.97[ASN][1000 genomes]
rs34846731	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36062390	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4581778	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233820	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73954904	0.97[ASN][1000 genomes]
rs73958215	0.97[ASN][1000 genomes]
rs8084584	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8086196	0.97[ASN][1000 genomes]
rs8087104	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9675795	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807439	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]

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	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv2247	chr18:29370842-29415712	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12959996	KIAA1012	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29394400-29418200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr18:29400200-29415600	Weak transcription	Brain Angular Gyrus	brain
3	chr18:29402000-29415400	Weak transcription	Right Ventricle	heart
4	chr18:29402200-29414600	Weak transcription	Fetal Heart	heart
5	chr18:29402200-29417200	Weak transcription	Pancreas	Pancrea
6	chr18:29402400-29415400	Weak transcription	Ovary	ovary
7	chr18:29405200-29413600	Weak transcription	Fetal Stomach	stomach
8	chr18:29405400-29415200	Weak transcription	Small Intestine	intestine
9	chr18:29405600-29414800	Weak transcription	NH-A	brain
10	chr18:29405600-29481800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:29406000-29417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:29406200-29518600	Weak transcription	Fetal Brain Male	brain
13	chr18:29406600-29415800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr18:29406800-29415200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr18:29406800-29431600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr18:29407200-29414400	Weak transcription	Osteobl	bone
17	chr18:29407200-29415400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr18:29407400-29415400	Weak transcription	Fetal Kidney	kidney
19	chr18:29407400-29427400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr18:29407400-29429800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr18:29407400-29432000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:29407600-29413600	Weak transcription	Fetal Intestine Small	intestine
23	chr18:29407800-29415000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr18:29407800-29415400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr18:29407800-29431200	Weak transcription	Psoas Muscle	Psoas
26	chr18:29408000-29415400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr18:29408000-29416000	Weak transcription	Brain Substantia Nigra	brain
28	chr18:29408000-29418200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr18:29408000-29460200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr18:29408200-29414600	Weak transcription	Fetal Brain Female	brain
31	chr18:29408400-29415400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr18:29408400-29417400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr18:29408400-29420800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:29408600-29413800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:29408600-29415600	Weak transcription	Colon Smooth Muscle	Colon
36	chr18:29408600-29420000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr18:29408600-29471800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr18:29408800-29413600	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr18:29408800-29415800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr18:29408800-29419400	Strong transcription	Adipose Nuclei	Adipose
41	chr18:29408800-29419400	Strong transcription	Fetal Intestine Large	intestine
42	chr18:29409000-29418000	Weak transcription	Brain Germinal Matrix	brain
43	chr18:29409000-29420000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr18:29409000-29420000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr18:29409000-29439000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr18:29409000-29456600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:29409200-29419400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr18:29409200-29419600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr18:29409400-29416400	Weak transcription	HMEC	breast
50	chr18:29409600-29430000	Strong transcription	Primary monocytes fromperipheralblood	blood

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