Variant report

Variant	rs3092963
Chromosome Location	chr3:46396938-46396939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr3:46396326-46397026	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46395645..46397767-chr3:46399914..46402472,2	K562	blood:

Variant related genes	Relation type
CCR2	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1034382	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10865940	0.91[EUR][1000 genomes]
rs11130089	0.91[EUR][1000 genomes]
rs11711054	0.90[EUR][1000 genomes]
rs1799865	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040389	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2040390	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2097282	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2097283	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2097284	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157057	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2157059	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2213288	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2213291	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2213292	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2373226	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3092962	0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3092964	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3138042	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34148191	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34193387	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34505903	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35053103	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35465430	0.93[EUR][1000 genomes]
rs35675823	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35971655	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36030342	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3762823	0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3918358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3918359	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3918361	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4134396	0.84[EUR][1000 genomes]
rs4683198	0.82[EUR][1000 genomes]
rs62244827	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62244840	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62244848	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441953	0.82[EUR][1000 genomes]
rs6441961	0.91[EUR][1000 genomes]
rs6441962	0.91[EUR][1000 genomes]
rs6441963	0.88[CEU][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs6441964	0.89[EUR][1000 genomes]
rs6441968	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6441971	0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs6441972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67450950	0.80[ASN][1000 genomes]
rs6765031	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6767895	0.91[EUR][1000 genomes]
rs6771900	0.91[EUR][1000 genomes]
rs6775208	0.91[EUR][1000 genomes]
rs6785981	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788723	0.91[EUR][1000 genomes]
rs6794300	0.90[EUR][1000 genomes]
rs6801761	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs71615444	0.82[EUR][1000 genomes]
rs7372094	0.90[EUR][1000 genomes]
rs7374654	0.90[EUR][1000 genomes]
rs7374671	0.86[EUR][1000 genomes]
rs743660	0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs7626249	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs762789	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634816	0.91[EUR][1000 genomes]
rs768539	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs963045	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9813756	0.90[EUR][1000 genomes]
rs9818053	0.91[EUR][1000 genomes]
rs9852052	0.89[EUR][1000 genomes]
rs9856098	0.91[EUR][1000 genomes]
rs9875668	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3092963	C3orf45	cis	parietal	SCAN
rs3092963	DALRD3	cis	cerebellum	SCAN
rs3092963	KLHL18	cis	parietal	SCAN
rs3092963	SHISA5	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46390200-46397800	Enhancers	Fetal Thymus	thymus
2	chr3:46392400-46402600	Weak transcription	Spleen	Spleen
3	chr3:46394400-46401200	Weak transcription	Brain Substantia Nigra	brain
4	chr3:46395200-46397000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
5	chr3:46395400-46397000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr3:46395400-46398000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:46395600-46397000	Active TSS	Colonic Mucosa	Colon
8	chr3:46395600-46397200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:46395600-46397800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:46395800-46397000	Enhancers	Primary T cells from cord blood	blood
11	chr3:46395800-46398000	Active TSS	Duodenum Mucosa	Duodenum
12	chr3:46395800-46404200	Weak transcription	Right Atrium	heart
13	chr3:46396000-46397000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:46396000-46397200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:46396000-46397400	Weak transcription	GM12878-XiMat	blood
16	chr3:46396000-46398200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:46396000-46401000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:46396000-46422000	Weak transcription	Lung	lung
19	chr3:46396200-46397400	Weak transcription	Fetal Brain Male	brain
20	chr3:46396200-46398200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:46396200-46398400	Active TSS	Primary T cells fromperipheralblood	blood
22	chr3:46396400-46397600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:46396400-46398600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:46396400-46400800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:46396400-46401000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:46396600-46397400	Enhancers	Primary B cells from cord blood	blood
27	chr3:46396800-46397000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr3:46396800-46397000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:46396800-46397000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:46396800-46397000	Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:46396800-46397000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr3:46396800-46397200	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:46396800-46397800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:46396800-46401000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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