Variant report

Variant	rs12494693
Chromosome Location	chr3:112677529-112677530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1032726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1392785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4103791	0.82[CEU][hapmap]
rs4682125	0.82[CEU][hapmap]
rs4682448	0.82[AMR][1000 genomes]
rs6438120	0.82[CEU][hapmap]
rs6438122	0.82[CEU][hapmap]
rs6769091	0.81[CEU][hapmap]
rs6784838	0.82[CEU][hapmap]
rs7611690	0.83[CEU][hapmap]
rs7615462	0.85[CEU][hapmap]
rs7615572	0.82[CEU][hapmap]
rs7646849	0.82[CEU][hapmap]
rs9823363	0.82[CEU][hapmap]
rs9828321	0.80[AMR][1000 genomes]
rs9833991	0.82[CEU][hapmap]
rs9834353	0.82[CEU][hapmap]
rs9864295	0.82[CEU][hapmap]
rs9871985	0.82[CEU][hapmap]

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	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
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12494693	CD200R1	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112665200-112677800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:112667400-112677600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:112675800-112677600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr3:112675800-112678200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:112675800-112678600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:112675800-112682600	Weak transcription	Spleen	Spleen
7	chr3:112675800-112682800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:112676200-112682000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:112677000-112677600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:112677000-112677800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:112677000-112677800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:112677000-112677800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:112677200-112677600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:112677200-112677800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:112677200-112680200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:112677400-112677600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:112677400-112678200	Active TSS	GM12878-XiMat	blood
18	chr3:112677400-112679200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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