Variant report

Variant	rs9871743
Chromosome Location	chr3:121670405-121670406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 12 )

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]
rs9811389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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]

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	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9871743	CCDC58	cis	parietal	SCAN
rs9871743	HCLS1	cis	multi-tissue	Pritchard
rs9871743	IQCB1	cis	parietal	SCAN
rs9871743	GOLGB1	cis	multi-tissue	Pritchard
rs9871743	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs9871743	EAF2	cis	cerebellum	SCAN
rs9871743	IQCB1	cis	cerebellum	SCAN
rs9871743	SLC15A2	cis	parietal	SCAN
rs9871743	SLC15A2	cis	cerebellum	SCAN
rs9871743	OSBPL11	cis	cerebellum	SCAN
rs9871743	SLC15A2	cis	Muscle Skeletal	GTEx
rs9871743	SLC15A2	cis	Artery Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
2	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:121650600-121675600	Weak transcription	Brain Anterior Caudate	brain
4	chr3:121656800-121675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:121660200-121671600	Weak transcription	Left Ventricle	heart
6	chr3:121660200-121675200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:121660200-121676600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:121661800-121674800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:121667200-121674400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:121669400-121671400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:121669400-121671800	ZNF genes & repeats	GM12878-XiMat	blood
12	chr3:121669600-121670800	Enhancers	Fetal Intestine Large	intestine
13	chr3:121669600-121671800	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr3:121669600-121673200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr3:121669600-121673200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:121669800-121670600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:121669800-121671000	Enhancers	HepG2	liver
18	chr3:121669800-121672600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr3:121670000-121671200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:121670000-121671200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:121670000-121671400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr3:121670000-121671800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr3:121670200-121670600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:121670200-121671600	Weak transcription	Fetal Intestine Small	intestine
25	chr3:121670400-121670800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:121670400-121671200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:121670400-121686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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