Variant report

Variant	rs1326775
Chromosome Location	chr9:95359555-95359556
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	GATA3	chr9:95359070-95359778	MCF-7	breast:	n/a	n/a
2	GATA3	chr9:95359131-95359629	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr9:95359085-95359596	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr9:95359062-95359666	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95357901..95361208-chr9:95361655..95366316,4	K562	blood:
2	chr9:95358665..95360582-chr9:95362854..95364983,2	K562	blood:
3	chr9:95086096..95089995-chr9:95356601..95360082,3	K562	blood:
4	chr9:95354681..95356667-chr9:95358553..95361349,2	K562	blood:

Variant related genes	Relation type
CENPP	TF binding region
ENSG00000188312	Chromatin interaction
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10491806	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820997	0.83[ASW][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs10820998	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10821001	0.87[AMR][1000 genomes]
rs10821003	0.87[AMR][1000 genomes]
rs10821004	0.87[AMR][1000 genomes]
rs10821005	0.87[AMR][1000 genomes]
rs10821009	0.84[MEX][hapmap]
rs10821011	0.86[AMR][1000 genomes]
rs10821012	0.84[MEX][hapmap]
rs10821014	0.87[AMR][1000 genomes]
rs10992367	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992380	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992382	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10992384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10992390	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992392	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][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];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992396	0.88[AMR][1000 genomes]
rs10992406	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs10992407	0.84[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs10992408	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10992409	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10992412	0.88[AMR][1000 genomes]
rs10992414	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs10992416	0.87[AMR][1000 genomes]
rs10992417	0.87[AMR][1000 genomes]
rs10992420	0.87[AMR][1000 genomes]
rs10992422	0.87[AMR][1000 genomes]
rs10992423	0.87[AMR][1000 genomes]
rs10992434	0.84[MEX][hapmap]
rs10992437	0.87[AMR][1000 genomes]
rs10992444	0.84[MEX][hapmap]
rs10992445	0.84[MEX][hapmap]
rs10992447	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs10992448	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs10992453	0.84[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes]
rs10992460	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs10992461	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1117670	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11533010	0.87[AMR][1000 genomes]
rs12236013	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12236754	0.82[CEU][hapmap];0.87[CHB][hapmap];0.83[AMR][1000 genomes]
rs12238691	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs12684587	0.80[AMR][1000 genomes]
rs12685080	0.88[YRI][hapmap]
rs12685257	0.84[MEX][hapmap]
rs12685358	0.87[AMR][1000 genomes]
rs12685780	0.84[MEX][hapmap]
rs12686771	0.84[CEU][hapmap];0.93[TSI][hapmap]
rs12686780	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12686781	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1323523	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1552908	0.80[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs1575460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17366488	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1853468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1874128	0.83[ASW][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs1980705	0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs2038685	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2038686	0.81[ASN][1000 genomes]
rs2088054	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2088055	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2131919	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2146848	1.00[CEU][hapmap]
rs2148537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2172716	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2181584	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs2274413	0.80[ASN][1000 genomes]
rs2281888	0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs2296080	0.84[MEX][hapmap]
rs3203916	0.84[MEX][hapmap]
rs3739605	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs556	0.84[MEX][hapmap]
rs58952648	0.87[AMR][1000 genomes]
rs60498616	0.87[AMR][1000 genomes]
rs6479426	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs67601697	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7031163	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes]
rs753804	0.87[AMR][1000 genomes]
rs754600	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7853617	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7856147	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7857105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][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];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7857502	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7863882	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7863890	0.84[MEX][hapmap]
rs7869603	0.87[AMR][1000 genomes]
rs7875050	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs879812	0.84[MEX][hapmap]
rs912261	0.91[ASW][hapmap];0.94[CHB][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap]
rs912264	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs971984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1326775	ANKRD19	cis	cerebellum	SCAN
rs1326775	CENPP	cis	multi-tissue	Pritchard
rs1326775	OMD	cis	parietal	SCAN
rs1326775	FBP1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95347600-95365800	Weak transcription	Thymus	Thymus
2	chr9:95347800-95364000	Weak transcription	Left Ventricle	heart
3	chr9:95353000-95362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:95353200-95360600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:95354000-95362200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:95355600-95360400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:95355600-95360400	Weak transcription	Lung	lung
8	chr9:95355600-95360400	Weak transcription	Right Atrium	heart
9	chr9:95355600-95360400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr9:95355600-95362000	Weak transcription	Aorta	Aorta
11	chr9:95355600-95362800	Weak transcription	Right Ventricle	heart
12	chr9:95355800-95367000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:95356200-95362600	Weak transcription	Fetal Thymus	thymus
14	chr9:95356400-95359800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:95356400-95360200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:95356400-95360200	Weak transcription	NHDF-Ad	bronchial
17	chr9:95356400-95360600	Weak transcription	Adipose Nuclei	Adipose
18	chr9:95356400-95362000	Weak transcription	HSMMtube	muscle
19	chr9:95356400-95362400	Weak transcription	HSMM	muscle
20	chr9:95356600-95360000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:95356600-95360400	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:95356600-95360400	Weak transcription	Ovary	ovary
23	chr9:95356600-95360600	Weak transcription	Fetal Stomach	stomach
24	chr9:95356800-95360000	Weak transcription	Colon Smooth Muscle	Colon
25	chr9:95356800-95360400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:95357800-95360000	Weak transcription	HepG2	liver
27	chr9:95358400-95361000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr9:95358600-95360600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr9:95358800-95359600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr9:95359000-95360400	Weak transcription	Placenta	Placenta
31	chr9:95359200-95359600	Enhancers	Fetal Kidney	kidney
32	chr9:95359200-95360200	Enhancers	Fetal Heart	heart
33	chr9:95359200-95360600	Enhancers	Liver	Liver
34	chr9:95359200-95360800	Enhancers	Fetal Lung	lung
35	chr9:95359200-95362600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:95359400-95359600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:95359400-95359800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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