Variant report

Variant	rs4744141
Chromosome Location	chr9:95352140-95352141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10114912	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10114932	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10116241	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs10117680	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10118107	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10118939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10124058	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10125450	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10125587	0.96[CEU][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10429459	0.91[CEU][hapmap]
rs10453241	0.88[CEU][hapmap]
rs10491804	0.91[CEU][hapmap]
rs10514815	0.91[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs1075397	0.81[AMR][1000 genomes]
rs10761155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10761158	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs10761160	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10761163	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10761164	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10820971	0.87[CEU][hapmap]
rs10820980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10820986	0.84[CEU][hapmap]
rs10820989	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10820990	0.82[ASW][hapmap];0.84[CEU][hapmap];0.81[YRI][hapmap]
rs10820994	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821008	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992322	0.88[CEU][hapmap]
rs10992347	0.91[CEU][hapmap]
rs10992349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10992365	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992366	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10992375	0.85[EUR][1000 genomes]
rs10992393	0.95[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs10992457	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1121978	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11788511	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11788523	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11791339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11792019	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11793563	0.94[ASN][1000 genomes]
rs11794346	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12336415	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12336884	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12338938	0.87[CEU][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs12341817	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12342019	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12343820	0.87[CEU][hapmap]
rs13284106	0.83[EUR][1000 genomes]
rs13286566	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13301537	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13301652	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1535754	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs1535756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs1980848	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2026585	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2094281	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2104533	0.94[ASW][hapmap];0.88[CEU][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs2181585	0.81[CEU][hapmap]
rs2274966	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs2296666	0.82[ASW][hapmap];0.91[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2296667	0.88[CEU][hapmap]
rs2296669	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2296670	0.94[ASN][1000 genomes]
rs2516567	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs2516568	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2761677	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2761678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2761681	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs2895219	0.94[ASW][hapmap];0.88[CEU][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs3739606	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs3780347	0.80[EUR][1000 genomes]
rs3927488	0.80[EUR][1000 genomes]
rs4743873	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743874	0.87[CEU][hapmap]
rs4743875	0.95[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4744133	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs4744134	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs4744135	0.82[ASW][hapmap];0.91[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs4744136	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs4744137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4744138	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4744143	0.85[EUR][1000 genomes]
rs62572543	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6479422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6479423	0.82[EUR][1000 genomes]
rs7020104	0.95[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7022562	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7029939	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7031567	0.82[ASW][hapmap];0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7033333	0.93[ASN][1000 genomes]
rs7033979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7037075	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7037194	0.91[CEU][hapmap];0.80[MEX][hapmap]
rs7043984	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7045409	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7045572	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs724102	0.91[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs747628	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs747629	0.88[ASW][hapmap];0.88[CEU][hapmap]
rs7847534	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7847929	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7848391	0.84[CEU][hapmap]
rs7848399	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs7848472	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7849927	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7850528	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7852698	0.95[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs7860786	0.82[ASW][hapmap];0.91[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs7863049	0.87[AFR][1000 genomes]
rs7864575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7864630	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7865019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7865118	0.85[EUR][1000 genomes]
rs7868013	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7869521	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs7869742	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs7872610	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7872644	0.80[EUR][1000 genomes]
rs7873390	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7873397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8067	0.88[CEU][hapmap]
rs927865	0.82[ASW][hapmap];0.91[CEU][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs9299404	0.88[CEU][hapmap];0.80[MEX][hapmap]
rs9299405	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs968040	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs987553	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4744141	CENPP	cis	cerebellum	SCAN
rs4744141	ZNF484	cis	parietal	SCAN
rs4744141	NOL8	cis	cerebellum	SCAN
rs4744141	CENPP	cis	Esophagus Muscularis	GTEx
rs4744141	ZNF484	cis	cerebellum	SCAN
rs4744141	CENPP	cis	parietal	SCAN

Chromatin state (count:25 , 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	chr9:95348800-95355200	Weak transcription	Aorta	Aorta
4	chr9:95349200-95353400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:95350800-95352800	Enhancers	Fetal Stomach	stomach
6	chr9:95351000-95353400	Enhancers	Colon Smooth Muscle	Colon
7	chr9:95351400-95354000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr9:95351600-95352600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:95351600-95352600	Enhancers	Fetal Lung	lung
10	chr9:95351600-95353000	Enhancers	Primary hematopoietic stem cells	blood
11	chr9:95351800-95352400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr9:95351800-95352600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr9:95351800-95352600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr9:95351800-95353000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr9:95351800-95353000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:95351800-95353000	Enhancers	Fetal Intestine Large	intestine
17	chr9:95351800-95353000	Enhancers	Stomach Smooth Muscle	stomach
18	chr9:95351800-95353200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:95351800-95353200	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr9:95351800-95353400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:95351800-95353400	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:95351800-95353600	Enhancers	Adipose Nuclei	Adipose
23	chr9:95351800-95356600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:95352000-95352600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr9:95352000-95353000	Enhancers	HUES6 Cell Line	embryonic stem cell

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