Variant report

Variant	rs9811389
Chromosome Location	chr3:121672948-121672949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10049074	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10934562	0.86[AMR][1000 genomes]
rs10934568	0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10934570	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs1143670	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1143671	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1143672	0.83[AMR][1000 genomes]
rs11718322	0.85[AMR][1000 genomes]
rs11914993	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs11920521	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs11920547	0.83[AMR][1000 genomes]
rs12637573	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074085	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316301	0.83[AMR][1000 genomes]
rs1316397	0.83[AMR][1000 genomes]
rs1357531	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1881999	0.83[AMR][1000 genomes]
rs1882000	0.82[AMR][1000 genomes]
rs1882002	0.83[AMR][1000 genomes]
rs1882003	0.83[AMR][1000 genomes]
rs1882004	0.83[AMR][1000 genomes]
rs1920289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920302	0.83[AMR][1000 genomes]
rs1920317	0.83[AMR][1000 genomes]
rs1920318	0.83[AMR][1000 genomes]
rs1920319	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2049330	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2049331	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2141615	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs2178415	0.82[AMR][1000 genomes]
rs2257109	0.83[AMR][1000 genomes]
rs2257115	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2257119	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2257120	0.83[AMR][1000 genomes]
rs2257123	0.83[AMR][1000 genomes]
rs2257124	0.83[AMR][1000 genomes]
rs2257132	0.83[AMR][1000 genomes]
rs2257212	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2257214	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2262494	0.83[AMR][1000 genomes]
rs2293612	0.83[AMR][1000 genomes]
rs2293614	0.83[AMR][1000 genomes]
rs2293615	0.83[AMR][1000 genomes]
rs2293616	0.95[MEX][hapmap];0.83[AMR][1000 genomes]
rs2332034	0.85[EUR][1000 genomes]
rs2332036	0.89[MEX][hapmap]
rs2332044	0.83[AMR][1000 genomes]
rs2332046	0.83[AMR][1000 genomes]
rs2332049	0.83[AMR][1000 genomes]
rs2332050	0.83[AMR][1000 genomes]
rs2332051	0.83[AMR][1000 genomes]
rs2332052	0.83[AMR][1000 genomes]
rs2332053	0.82[AMR][1000 genomes]
rs2332054	0.82[AMR][1000 genomes]
rs2689272	0.83[AMR][1000 genomes]
rs2689273	0.83[AMR][1000 genomes]
rs2689281	0.83[AMR][1000 genomes]
rs2689282	0.83[AMR][1000 genomes]
rs2689283	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2689284	0.83[AMR][1000 genomes]
rs2689287	0.83[AMR][1000 genomes]
rs2689288	0.83[AMR][1000 genomes]
rs2689289	0.83[AMR][1000 genomes]
rs2689291	0.83[AMR][1000 genomes]
rs2689292	0.83[AMR][1000 genomes]
rs2700416	0.83[AMR][1000 genomes]
rs2700420	0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs2700421	0.83[AMR][1000 genomes]
rs2700425	0.83[AMR][1000 genomes]
rs2700426	0.83[AMR][1000 genomes]
rs2877566	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2877568	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs2877569	0.82[AMR][1000 genomes]
rs3762819	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs3762821	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs3762822	0.83[AMR][1000 genomes]
rs3792596	0.83[AMR][1000 genomes]
rs3792597	0.87[AMR][1000 genomes]
rs3805134	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs3805138	0.82[AMR][1000 genomes]
rs3817601	0.83[AMR][1000 genomes]
rs3932367	0.83[AMR][1000 genomes]
rs4325959	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4583698	0.82[AMR][1000 genomes]
rs59823080	0.87[AMR][1000 genomes]
rs6438687	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs6765799	0.83[AMR][1000 genomes]
rs6780234	0.82[AMR][1000 genomes]
rs6791876	0.81[AMR][1000 genomes]
rs6793566	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6793858	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6794360	0.81[AMR][1000 genomes]
rs6803757	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs7635449	0.82[AMR][1000 genomes]
rs7637569	0.90[MEX][hapmap];0.83[AMR][1000 genomes]
rs866926	0.83[AMR][1000 genomes]
rs866927	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs866929	0.83[AMR][1000 genomes]
rs874741	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs874742	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs9289181	0.82[AMR][1000 genomes]
rs9289182	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs9289183	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs9811473	0.83[AMR][1000 genomes]
rs9812515	0.83[AMR][1000 genomes]
rs9812694	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9812869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815756	0.82[AMR][1000 genomes]
rs9816071	0.83[AMR][1000 genomes]
rs9816215	0.82[AMR][1000 genomes]
rs9816720	0.84[MEX][hapmap]
rs9822474	0.86[AMR][1000 genomes]
rs9824120	0.81[CEU][hapmap];0.87[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs9825193	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9827390	0.82[AMR][1000 genomes]
rs9828753	0.83[AMR][1000 genomes]
rs9829070	0.83[AMR][1000 genomes]
rs9830721	0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs9835875	0.82[AMR][1000 genomes]
rs9836339	0.83[AMR][1000 genomes]
rs9844039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9845790	0.86[AMR][1000 genomes]
rs9850685	0.85[AMR][1000 genomes]
rs9856253	0.83[AMR][1000 genomes]
rs9862977	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs9863154	0.86[EUR][1000 genomes]
rs9863155	0.83[AMR][1000 genomes]
rs9866936	0.83[AMR][1000 genomes]
rs9867460	0.87[AMR][1000 genomes]
rs9870245	0.86[AMR][1000 genomes]
rs9871534	0.83[AMR][1000 genomes]
rs9871743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9811389	SLC15A2	cis	cerebellum	SCAN
rs9811389	EAF2	cis	multi-tissue	Pritchard
rs9811389	IQCB1	cis	parietal	SCAN
rs9811389	GOLGB1	cis	multi-tissue	Pritchard
rs9811389	SLC15A2	cis	Muscle Skeletal	GTEx
rs9811389	PARP14	cis	multi-tissue	Pritchard
rs9811389	HCLS1	cis	multi-tissue	Pritchard
rs9811389	EAF2	cis	cerebellum	SCAN
rs9811389	CCDC58	cis	parietal	SCAN
rs9811389	IQCB1	cis	cerebellum	SCAN
rs9811389	SLC15A2	cis	Artery Tibial	GTEx
rs9811389	OSBPL11	cis	cerebellum	SCAN
rs9811389	SLC15A2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121650600-121675600	Weak transcription	Brain Anterior Caudate	brain
2	chr3:121656800-121675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:121660200-121675200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:121660200-121676600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:121661800-121674800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:121667200-121674400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:121669600-121673200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr3:121669600-121673200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:121670400-121686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:121670600-121675000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:121671200-121676800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:121671400-121673600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
13	chr3:121671800-121673000	Weak transcription	GM12878-XiMat	blood
14	chr3:121671800-121675000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:121671800-121675400	Weak transcription	Pancreas	Pancrea
16	chr3:121672200-121673400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:121672600-121673200	Strong transcription	Primary B cells from cord blood	blood
18	chr3:121672600-121673200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr3:121672800-121673400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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