Variant report

Variant	rs4682120
Chromosome Location	chr3:112575080-112575081
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1016348	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs10934190	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497951	0.84[ASN][1000 genomes]
rs13326243	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387023	0.86[CHB][hapmap]
rs1387024	0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs1392786	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1466872	0.83[ASN][1000 genomes]
rs1488193	0.91[CHB][hapmap]
rs1500878	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1500879	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1844084	0.95[CHB][hapmap]
rs1971986	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2087284	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2101440	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171509	0.83[ASN][1000 genomes]
rs2399436	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2399443	0.99[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28859668	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28867393	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4103791	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4234417	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4478054	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4571210	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4682125	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4682440	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682441	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682444	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682447	0.91[CHB][hapmap]
rs6438111	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6438112	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6438113	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6438114	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6438118	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs6438119	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs6438120	1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs6438122	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6765379	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6766388	0.99[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769091	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6772799	0.83[ASN][1000 genomes]
rs6784838	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs6791158	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791672	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808249	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7355890	0.83[ASN][1000 genomes]
rs7611690	0.83[ASN][1000 genomes]
rs7615462	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7615572	0.81[ASW][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs7622812	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7622814	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7632218	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646849	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7652504	0.83[ASN][1000 genomes]
rs7652536	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815606	0.83[ASN][1000 genomes]
rs9818564	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9819079	0.81[ASN][1000 genomes]
rs9823363	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9826308	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9833991	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9834353	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9834840	0.84[ASN][1000 genomes]
rs9838082	0.80[AFR][1000 genomes]
rs9847365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854885	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9864295	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9865242	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9868053	0.83[ASN][1000 genomes]
rs9868839	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9870335	0.84[ASN][1000 genomes]
rs9870568	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs9871985	1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs9875551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9877631	0.84[ASN][1000 genomes]
rs9883255	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3501334	chr3:112546820-112648766	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3501335	chr3:112546820-112648766	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4682120	CD200R1	cis	multi-tissue	Pritchard

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112567800-112575200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:112570000-112575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:112574400-112578200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:112574600-112576000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:112574600-112576000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:112574600-112578600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:112574800-112576800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:112574800-112577600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:112574800-112578400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:112575000-112576000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr3:112575000-112576000	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:112575000-112576000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:112575000-112576200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:112575000-112576800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:112575000-112577800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:112575000-112578000	Enhancers	Primary B cells from peripheral blood	blood

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