Variant report

Variant	rs2476439
Chromosome Location	chr9:102908076-102908077
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:178)

rs_ID	r²[population]
rs10116798	0.96[ASN][1000 genomes]
rs10117150	0.96[ASN][1000 genomes]
rs1014651	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1014652	0.93[ASN][1000 genomes]
rs10156395	0.81[ASN][1000 genomes]
rs10739795	0.89[ASN][1000 genomes]
rs10739796	0.94[ASN][1000 genomes]
rs10760710	0.89[ASN][1000 genomes]
rs10760711	0.93[ASN][1000 genomes]
rs10760712	0.89[ASN][1000 genomes]
rs10760720	0.96[ASN][1000 genomes]
rs10819714	0.93[ASN][1000 genomes]
rs10819715	0.93[ASN][1000 genomes]
rs10819716	0.89[ASN][1000 genomes]
rs10819717	0.89[ASN][1000 genomes]
rs10819719	0.87[ASN][1000 genomes]
rs10819737	0.96[ASN][1000 genomes]
rs10819739	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988945	0.93[ASN][1000 genomes]
rs10988963	0.89[ASN][1000 genomes]
rs10988968	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10988969	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10988973	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10988974	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10989009	0.96[ASN][1000 genomes]
rs1099908	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1099909	0.86[ASN][1000 genomes]
rs1099910	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12336751	0.96[ASN][1000 genomes]
rs12552646	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12685650	0.93[ASN][1000 genomes]
rs13301295	0.96[ASN][1000 genomes]
rs1338119	0.93[ASN][1000 genomes]
rs1338121	0.81[AMR][1000 genomes]
rs1338126	0.81[AMR][1000 genomes]
rs1342147	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1361668	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1406613	0.89[ASN][1000 genomes]
rs1415926	0.94[ASN][1000 genomes]
rs1418267	0.89[ASN][1000 genomes]
rs1529191	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1529192	0.89[ASN][1000 genomes]
rs1529193	0.89[ASN][1000 genomes]
rs1534726	0.87[ASN][1000 genomes]
rs1535667	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539297	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1572607	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1578644	0.89[ASN][1000 genomes]
rs1578645	0.89[ASN][1000 genomes]
rs1578646	0.93[ASN][1000 genomes]
rs1852864	0.89[ASN][1000 genomes]
rs1852865	0.89[ASN][1000 genomes]
rs1891334	0.81[ASN][1000 genomes]
rs1999877	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057476	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2065997	0.81[AMR][1000 genomes]
rs2093696	0.93[ASN][1000 genomes]
rs2096158	0.89[ASN][1000 genomes]
rs2104273	0.89[ASN][1000 genomes]
rs2181579	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2209082	0.86[ASN][1000 genomes]
rs2476441	0.96[ASN][1000 genomes]
rs2476442	0.96[ASN][1000 genomes]
rs2491095	0.93[ASN][1000 genomes]
rs2491096	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2491098	0.81[AMR][1000 genomes]
rs2698999	0.88[ASN][1000 genomes]
rs2761053	0.85[ASN][1000 genomes]
rs2761056	0.93[ASN][1000 genomes]
rs2787361	0.89[ASN][1000 genomes]
rs2787363	0.91[ASN][1000 genomes]
rs2787364	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2787365	0.93[ASN][1000 genomes]
rs2787366	0.93[ASN][1000 genomes]
rs2787379	0.81[AMR][1000 genomes]
rs2787382	0.81[AMR][1000 genomes]
rs2787384	0.81[AMR][1000 genomes]
rs2787386	0.81[AMR][1000 genomes]
rs2787391	0.83[ASN][1000 genomes]
rs2787393	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2787394	0.87[ASN][1000 genomes]
rs2787395	0.87[ASN][1000 genomes]
rs2787396	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2787397	0.87[ASN][1000 genomes]
rs2791335	0.88[ASN][1000 genomes]
rs2791336	0.93[ASN][1000 genomes]
rs2791337	0.93[ASN][1000 genomes]
rs2795575	0.93[ASN][1000 genomes]
rs2806681	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806682	0.93[ASN][1000 genomes]
rs2806683	0.91[ASN][1000 genomes]
rs2806684	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2806685	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2806687	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2806688	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2806689	0.82[AMR][1000 genomes]
rs2806690	0.81[AMR][1000 genomes]
rs2806691	0.81[AMR][1000 genomes]
rs28448789	0.89[ASN][1000 genomes]
rs35493819	0.81[ASN][1000 genomes]
rs3824510	0.81[ASN][1000 genomes]
rs41346545	0.93[ASN][1000 genomes]
rs4495492	0.86[ASN][1000 genomes]
rs4503155	0.89[ASN][1000 genomes]
rs4517187	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4742779	0.93[ASN][1000 genomes]
rs4743375	0.89[ASN][1000 genomes]
rs4743376	0.89[ASN][1000 genomes]
rs4743378	0.81[ASN][1000 genomes]
rs4743379	0.89[ASN][1000 genomes]
rs4743380	0.89[ASN][1000 genomes]
rs4743381	0.86[ASN][1000 genomes]
rs4743382	0.93[ASN][1000 genomes]
rs4743384	0.81[ASN][1000 genomes]
rs4743386	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6478991	0.89[ASN][1000 genomes]
rs6478994	0.89[ASN][1000 genomes]
rs6478995	0.89[ASN][1000 genomes]
rs6478996	0.89[ASN][1000 genomes]
rs6478997	0.89[ASN][1000 genomes]
rs6478998	0.89[ASN][1000 genomes]
rs6479000	0.89[ASN][1000 genomes]
rs6479001	0.85[ASN][1000 genomes]
rs6479002	0.85[ASN][1000 genomes]
rs7018981	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7022493	0.89[ASN][1000 genomes]
rs7024016	0.89[ASN][1000 genomes]
rs7025300	0.89[ASN][1000 genomes]
rs7026532	0.89[ASN][1000 genomes]
rs7027414	0.89[ASN][1000 genomes]
rs7029020	0.89[ASN][1000 genomes]
rs7029048	0.89[ASN][1000 genomes]
rs7032333	0.89[ASN][1000 genomes]
rs7033091	0.89[ASN][1000 genomes]
rs7036518	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7037362	0.89[ASN][1000 genomes]
rs7041338	0.89[ASN][1000 genomes]
rs7042194	0.93[ASN][1000 genomes]
rs7042912	0.89[ASN][1000 genomes]
rs7043057	0.89[ASN][1000 genomes]
rs7044219	0.89[ASN][1000 genomes]
rs7045612	0.81[ASN][1000 genomes]
rs7047092	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7846794	0.85[ASN][1000 genomes]
rs7847213	0.85[ASN][1000 genomes]
rs7853485	0.87[ASN][1000 genomes]
rs7856844	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857530	0.89[ASN][1000 genomes]
rs7858606	0.93[ASN][1000 genomes]
rs7859492	0.94[ASN][1000 genomes]
rs7861003	0.85[ASN][1000 genomes]
rs7862460	0.93[ASN][1000 genomes]
rs7870585	0.91[ASN][1000 genomes]
rs7874449	0.89[ASN][1000 genomes]
rs846752	0.96[ASN][1000 genomes]
rs846753	0.94[ASN][1000 genomes]
rs846754	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846755	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs846756	0.85[ASN][1000 genomes]
rs846758	0.85[ASN][1000 genomes]
rs846759	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs846761	0.85[ASN][1000 genomes]
rs846762	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs846763	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs846765	0.85[ASN][1000 genomes]
rs846766	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs846768	0.96[ASN][1000 genomes]
rs846769	0.96[ASN][1000 genomes]
rs846770	0.96[ASN][1000 genomes]
rs860171	0.94[ASN][1000 genomes]
rs863668	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299337	0.87[ASN][1000 genomes]
rs9408993	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9408995	0.91[ASN][1000 genomes]
rs9409325	0.87[ASN][1000 genomes]
rs942163	0.93[ASN][1000 genomes]
rs9695692	0.96[ASN][1000 genomes]
rs9886877	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2476439	INVS	cis	multi-tissue	Pritchard
rs2476439	STX17	cis	Esophagus Mucosa	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102874200-102912600	Weak transcription	Osteobl	bone
2	chr9:102874200-102937600	Weak transcription	Aorta	Aorta
3	chr9:102879800-102935000	Weak transcription	Ovary	ovary
4	chr9:102883000-102937600	Weak transcription	Fetal Intestine Large	intestine
5	chr9:102883800-102928400	Weak transcription	Primary T cells from cord blood	blood
6	chr9:102885200-102932600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:102886000-102931600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:102887800-102922200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:102889200-102936000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:102889600-102934600	Weak transcription	Fetal Intestine Small	intestine
11	chr9:102891800-102935200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:102892200-102909200	Weak transcription	Fetal Stomach	stomach
13	chr9:102893000-102934600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:102893800-102936200	Weak transcription	Primary B cells from cord blood	blood
15	chr9:102895200-102920600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:102905000-102908800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr9:102905200-102908800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:102905200-102908800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:102905600-102909000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:102905800-102908600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:102905800-102909000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:102906000-102908600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr9:102906000-102908800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr9:102906400-102908400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:102906400-102908800	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr9:102906600-102908800	Active TSS	H1 Cell Line	embryonic stem cell
27	chr9:102906600-102908800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:102906600-102908800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr9:102907000-102909600	Enhancers	K562	blood
30	chr9:102907800-102908200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr9:102908000-102908400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:102908000-102908600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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