Variant report

Variant	rs17462606
Chromosome Location	chr9:95370664-95370665
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	TCF12	chr9:95369832-95370750	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr9:95369236-95370690	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr9:95369798-95370693	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95368898..95371763-chr9:95431399..95433755,2	MCF-7	breast:
2	chr9:95368081..95371293-chr9:95378111..95381332,3	MCF-7	breast:
3	chr9:95364179..95365756-chr9:95368617..95371594,2	K562	blood:
4	chr9:95369063..95371950-chr9:95374087..95377322,4	K562	blood:

Variant related genes	Relation type
CENPP	TF binding region
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs17365144	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17366134	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17519453	0.86[ASN][1000 genomes]
rs2277165	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2277167	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2277170	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34860658	0.86[ASN][1000 genomes]
rs3780348	1.00[CHD][hapmap]
rs3802383	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41266685	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41273374	0.81[EUR][1000 genomes]
rs41305495	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41312236	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72752435	0.82[ASN][1000 genomes]
rs72752467	0.82[ASN][1000 genomes]
rs72752474	0.86[ASN][1000 genomes]
rs72754429	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72754430	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754433	0.85[AMR][1000 genomes]
rs72754434	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754435	0.85[AMR][1000 genomes]
rs72754436	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754437	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754440	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754442	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754443	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754444	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754445	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754446	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754447	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754450	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72754452	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754457	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754461	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754463	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754464	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72754465	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754470	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754477	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754480	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72754482	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754483	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754485	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72754487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72754489	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754491	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754493	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72754496	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72754499	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72754501	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72756403	0.92[AMR][1000 genomes]
rs72756404	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72756405	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72756406	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72756408	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72756410	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72756414	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72756415	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72756416	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756418	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72756423	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72756424	0.92[AMR][1000 genomes]
rs72756425	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72756426	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72756427	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72756431	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72756433	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756437	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72756438	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756440	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756441	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756442	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756443	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756444	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72756446	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756447	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756448	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756452	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756455	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756457	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756458	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756459	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756460	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756462	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756464	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756465	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756467	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756468	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756469	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72756471	0.81[EUR][1000 genomes]
rs72756478	0.81[EUR][1000 genomes]
rs72756483	0.81[EUR][1000 genomes]
rs72756486	0.81[EUR][1000 genomes]
rs72756489	0.81[EUR][1000 genomes]
rs72756497	0.81[EUR][1000 genomes]
rs72756498	0.81[EUR][1000 genomes]
rs72756500	0.81[EUR][1000 genomes]
rs72758504	0.81[EUR][1000 genomes]
rs72758505	0.81[EUR][1000 genomes]
rs72758508	0.81[EUR][1000 genomes]
rs72758519	0.81[EUR][1000 genomes]
rs72758524	0.81[EUR][1000 genomes]
rs72758525	0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17462606	HOOK1	trans	lymphoblastoid	seeQTL
rs17462606	F12	trans	lymphoblastoid	seeQTL
rs17462606	NOTCH2	trans	lymphoblastoid	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95362800-95373000	Weak transcription	HMEC	breast
2	chr9:95363000-95371400	Weak transcription	Right Ventricle	heart
3	chr9:95363200-95371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:95363400-95374000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:95363400-95396000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:95364000-95372800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:95364400-95372800	Weak transcription	NHEK	skin
8	chr9:95366200-95373000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:95366400-95370800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:95366400-95371400	Weak transcription	Esophagus	oesophagus
11	chr9:95366400-95375000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:95366600-95373600	Weak transcription	Thymus	Thymus
13	chr9:95367400-95373800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:95367400-95380600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:95368600-95371600	Enhancers	Osteobl	bone
16	chr9:95368600-95371800	Enhancers	Fetal Kidney	kidney
17	chr9:95368600-95372000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:95368600-95372000	Enhancers	Colon Smooth Muscle	Colon
19	chr9:95368800-95371400	Enhancers	Stomach Smooth Muscle	stomach
20	chr9:95369000-95372800	Enhancers	Fetal Muscle Leg	muscle
21	chr9:95369000-95373200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr9:95369200-95372000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:95369200-95372200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:95369400-95371200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:95369400-95371400	Enhancers	NHLF	lung
26	chr9:95369400-95372000	Enhancers	Brain Hippocampus Middle	brain
27	chr9:95369400-95372000	Enhancers	Rectal Smooth Muscle	rectum
28	chr9:95369400-95372600	Enhancers	Fetal Stomach	stomach
29	chr9:95369400-95372800	Enhancers	Adipose Nuclei	Adipose
30	chr9:95369400-95373800	Enhancers	NHDF-Ad	bronchial
31	chr9:95369600-95370800	Enhancers	HSMM	muscle
32	chr9:95369600-95371400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:95369600-95371600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:95369600-95371800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:95369600-95371800	Enhancers	Brain Angular Gyrus	brain
36	chr9:95369600-95372000	Enhancers	Brain Anterior Caudate	brain
37	chr9:95369600-95372400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:95369600-95373000	Weak transcription	Small Intestine	intestine
39	chr9:95369600-95373200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr9:95369800-95371000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr9:95369800-95371200	Enhancers	NH-A	brain
42	chr9:95369800-95372000	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr9:95369800-95374200	Weak transcription	Liver	Liver
44	chr9:95369800-95374200	Weak transcription	GM12878-XiMat	blood
45	chr9:95370000-95371000	Enhancers	HepG2	liver
46	chr9:95370000-95371800	Enhancers	Aorta	Aorta
47	chr9:95370000-95371800	Enhancers	Pancreas	Pancrea
48	chr9:95370000-95372000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:95370000-95372000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr9:95370000-95372000	Enhancers	Fetal Lung	lung

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