Variant report

Variant	rs9425586
Chromosome Location	chr1:172351052-172351053
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	chr1:172350982-172351579	SK-N-SH	brain:	n/a	n/a
2	TCF7L2	chr1:172351014-172351096	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172348750..172351497-chr1:172354142..172356415,3	K562	blood:
2	chr1:172348015..172349908-chr1:172350269..172352260,2	K562	blood:
3	chr1:172345198..172346938-chr1:172350887..172353536,2	K562	blood:
4	chr1:172345890..172347639-chr1:172350448..172352485,2	MCF-7	breast:

Variant related genes	Relation type
PIGC	TF binding region
ENSG00000197959	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1011731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1023479	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489284	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10752943	0.95[ASN][1000 genomes]
rs10752944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10797996	0.97[ASN][1000 genomes]
rs10911654	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10911681	0.95[ASN][1000 genomes]
rs10911684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10911792	0.90[CHB][hapmap]
rs12404665	0.97[ASN][1000 genomes]
rs12405515	0.90[ASN][1000 genomes]
rs1894633	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2001127	0.93[ASN][1000 genomes]
rs2001128	0.93[ASN][1000 genomes]
rs2001129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2213731	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2213732	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2227198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2227199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2227200	0.95[ASN][1000 genomes]
rs2269612	0.97[ASN][1000 genomes]
rs2301453	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3213564	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768445	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4471302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4504922	0.94[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4916251	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916252	0.97[ASN][1000 genomes]
rs4916253	0.93[ASN][1000 genomes]
rs4916254	0.86[ASN][1000 genomes]
rs4916263	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916264	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs4916265	0.90[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs57668887	0.80[ASN][1000 genomes]
rs6424894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6676665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698987	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6700575	0.95[ASN][1000 genomes]
rs714515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73046851	0.83[ASN][1000 genomes]
rs7517737	0.93[ASN][1000 genomes]
rs7518039	0.94[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7539464	0.93[ASN][1000 genomes]
rs7539972	0.94[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7544610	0.97[ASN][1000 genomes]
rs7546252	0.93[ASN][1000 genomes]
rs9286854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425269	1.00[JPT][hapmap]
rs9425291	0.89[CHB][hapmap]
rs9425297	0.92[ASN][1000 genomes]
rs9425298	0.93[ASN][1000 genomes]
rs9425299	0.93[ASN][1000 genomes]
rs9425300	0.93[ASN][1000 genomes]
rs9425301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425573	0.82[ASN][1000 genomes]
rs9425575	0.83[ASN][1000 genomes]
rs9425579	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9425587	0.97[ASN][1000 genomes]
rs9425589	0.97[ASN][1000 genomes]
rs9425590	0.90[ASN][1000 genomes]
rs9425591	0.93[ASN][1000 genomes]
rs9425592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425628	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs979935	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs991790	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9425586	KIFAP3	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172343600-172352200	Weak transcription	HSMM	muscle
2	chr1:172343600-172359800	Weak transcription	Brain Angular Gyrus	brain
3	chr1:172344800-172352400	Weak transcription	Brain Anterior Caudate	brain
4	chr1:172344800-172357800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:172344800-172359000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:172345800-172351200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:172345800-172352200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:172346600-172367400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:172347400-172357600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:172348000-172351200	Weak transcription	NHDF-Ad	bronchial
11	chr1:172348000-172351600	Weak transcription	Ovary	ovary
12	chr1:172348200-172351600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:172348600-172351800	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:172348600-172353600	Enhancers	Fetal Lung	lung
15	chr1:172349400-172351400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:172349600-172351800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr1:172349600-172352200	Enhancers	Colon Smooth Muscle	Colon
18	chr1:172349600-172353600	Enhancers	Fetal Stomach	stomach
19	chr1:172349600-172353800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:172349600-172356400	Enhancers	Fetal Kidney	kidney
21	chr1:172349600-172362000	Weak transcription	Left Ventricle	heart
22	chr1:172349800-172351400	Enhancers	Fetal Intestine Small	intestine
23	chr1:172349800-172353600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:172349800-172353800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:172349800-172353800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:172349800-172363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:172350000-172354000	Enhancers	Fetal Muscle Leg	muscle
28	chr1:172350200-172352200	Weak transcription	Osteobl	bone
29	chr1:172350200-172353800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr1:172350400-172351200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:172350400-172351200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:172350400-172351200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:172350400-172351400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:172350400-172351400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:172350400-172351400	Enhancers	Primary hematopoietic stem cells	blood
36	chr1:172350400-172351400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:172350400-172351600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr1:172350400-172351600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr1:172350400-172351800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:172350400-172352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:172350400-172352000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:172350400-172352000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:172350400-172352000	Weak transcription	NH-A	brain
44	chr1:172350400-172352200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:172350400-172352600	Enhancers	HUVEC	blood vessel
46	chr1:172350400-172353000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:172350400-172353200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:172350400-172353800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:172350400-172354400	Weak transcription	Thymus	Thymus
50	chr1:172350400-172357600	Weak transcription	Brain Hippocampus Middle	brain

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