Variant report

Variant	rs10992453
Chromosome Location	chr9:95524833-95524834
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95490365..95492955-chr9:95524565..95526650,2	K562	blood:
2	chr9:95502006..95503566-chr9:95523305..95525520,2	K562	blood:
3	chr9:95428069..95433526-chr9:95524054..95531235,7	MCF-7	breast:
4	chr9:95521437..95523022-chr9:95523421..95525145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 160 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs1010823	0.85[ASN][1000 genomes]
rs1040977	0.80[EUR][1000 genomes]
rs10820998	0.84[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10821001	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821002	0.82[ASN][1000 genomes]
rs10821003	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821004	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10821005	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821007	0.84[ASN][1000 genomes]
rs10821009	0.88[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10821010	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10821011	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821012	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10821014	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821015	0.85[ASN][1000 genomes]
rs10821016	0.85[ASN][1000 genomes]
rs10992380	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs10992382	0.88[CHB][hapmap]
rs10992384	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs10992390	0.86[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992392	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10992396	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992404	0.85[ASN][1000 genomes]
rs10992406	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992407	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992408	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10992409	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10992412	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10992413	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10992414	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992416	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992417	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992418	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10992419	0.82[ASN][1000 genomes]
rs10992420	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992422	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992423	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992426	0.93[ASN][1000 genomes]
rs10992427	0.82[ASN][1000 genomes]
rs10992430	0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992431	0.84[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992432	0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs10992433	0.94[ASN][1000 genomes]
rs10992434	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10992436	0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992437	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992438	0.85[ASN][1000 genomes]
rs10992441	0.85[ASN][1000 genomes]
rs10992442	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992443	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992444	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992445	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992447	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10992448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992451	0.83[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs10992456	0.85[ASN][1000 genomes]
rs10992460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992462	0.85[ASN][1000 genomes]
rs10992469	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs10992474	0.87[EUR][1000 genomes]
rs10992476	0.88[EUR][1000 genomes]
rs1117670	0.88[CHB][hapmap]
rs1125063	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs1125064	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11533010	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11535540	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12057034	0.88[EUR][1000 genomes]
rs12236013	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12236393	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12236516	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12236747	0.85[ASN][1000 genomes]
rs12236754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236788	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12237216	0.83[ASN][1000 genomes]
rs12238691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12683944	0.85[ASN][1000 genomes]
rs12684076	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12684587	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12685256	0.82[ASN][1000 genomes]
rs12685257	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12685358	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685780	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12685791	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12686058	0.84[ASN][1000 genomes]
rs12686771	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12686781	0.80[AMR][1000 genomes]
rs1323523	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1326775	0.84[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes]
rs1407944	0.96[ASN][1000 genomes]
rs1555574	0.82[AMR][1000 genomes]
rs1575460	0.86[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs16908555	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs16908560	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17366488	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1853428	0.92[CEU][hapmap]
rs1853429	0.88[EUR][1000 genomes]
rs1853468	0.84[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes]
rs1974004	0.92[CEU][hapmap]
rs2038685	0.84[AMR][1000 genomes]
rs2146848	0.86[CEU][hapmap]
rs2148537	0.84[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes]
rs2181584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181586	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2277164	0.89[ASN][1000 genomes]
rs2296080	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2398780	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs3203916	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3739605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141966	0.88[EUR][1000 genomes]
rs4545157	0.85[ASN][1000 genomes]
rs556	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs56111209	0.85[ASN][1000 genomes]
rs56203846	0.82[ASN][1000 genomes]
rs56311406	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56339669	0.84[ASN][1000 genomes]
rs57421019	0.85[ASN][1000 genomes]
rs57720404	0.85[ASN][1000 genomes]
rs57737182	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58952648	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60173654	0.85[ASN][1000 genomes]
rs60457563	0.85[ASN][1000 genomes]
rs60498616	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479426	0.88[CHB][hapmap]
rs67601697	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68022962	0.85[ASN][1000 genomes]
rs68046436	0.85[ASN][1000 genomes]
rs7031163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037961	0.82[ASN][1000 genomes]
rs753802	0.83[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs753803	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs753804	0.86[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754600	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7850075	0.92[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7850871	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7851947	0.96[ASN][1000 genomes]
rs7853617	0.86[EUR][1000 genomes]
rs7855203	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7856147	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7857105	0.84[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7857502	0.86[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7859967	0.84[EUR][1000 genomes]
rs7860628	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7862106	0.84[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7863741	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7863882	0.88[CHB][hapmap]
rs7869529	0.82[ASN][1000 genomes]
rs7869603	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7871537	0.80[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs7875050	0.91[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7875225	0.82[JPT][hapmap]
rs8181065	0.84[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs878610	0.85[ASN][1000 genomes]
rs912259	0.85[ASN][1000 genomes]
rs912261	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs912264	0.86[CEU][hapmap];0.85[AMR][1000 genomes]
rs971984	0.84[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes]
rs976320	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs976321	0.85[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	nsv430081	chr9:95502571-95568110	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10992453	CENPP	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95512000-95525000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:95512400-95525200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:95512600-95525400	Weak transcription	A549	lung
4	chr9:95518400-95525000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:95518400-95525200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:95518400-95525200	Weak transcription	Fetal Intestine Small	intestine
7	chr9:95518600-95525200	Weak transcription	Fetal Intestine Large	intestine
8	chr9:95519200-95525200	Enhancers	Fetal Thymus	thymus
9	chr9:95519400-95525200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:95520400-95525600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:95520400-95526000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:95521400-95525000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr9:95521400-95525000	Enhancers	Thymus	Thymus
14	chr9:95521400-95525200	Enhancers	Brain Hippocampus Middle	brain
15	chr9:95521400-95525400	Enhancers	Brain Substantia Nigra	brain
16	chr9:95521600-95525000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr9:95521600-95525000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr9:95521600-95525200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr9:95521600-95525200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:95521600-95525200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:95521600-95525200	Enhancers	Right Ventricle	heart
22	chr9:95521600-95525400	Enhancers	Primary B cells from peripheral blood	blood
23	chr9:95521600-95525400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr9:95521600-95525600	Enhancers	Fetal Heart	heart
25	chr9:95521800-95525000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr9:95521800-95525000	Enhancers	Right Atrium	heart
27	chr9:95521800-95525200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:95521800-95525200	Enhancers	Pancreas	Pancrea
29	chr9:95521800-95525400	Enhancers	Left Ventricle	heart
30	chr9:95521800-95525400	Enhancers	Ovary	ovary
31	chr9:95521800-95525800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:95521800-95525800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr9:95521800-95526000	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr9:95522000-95525000	Enhancers	Colon Smooth Muscle	Colon
35	chr9:95522000-95525200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr9:95522000-95525400	Enhancers	Liver	Liver
37	chr9:95522000-95525600	Enhancers	Lung	lung
38	chr9:95522400-95525600	Enhancers	Placenta	Placenta
39	chr9:95522600-95525000	Enhancers	HepG2	liver
40	chr9:95522600-95525200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:95522600-95525400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:95523000-95525200	Enhancers	Gastric	stomach
43	chr9:95523000-95526400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:95523000-95526400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:95523200-95525200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:95523200-95525400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr9:95523400-95525800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:95523600-95525400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:95523600-95525400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr9:95523600-95525400	Enhancers	Rectal Mucosa Donor 31	rectum

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