Variant report

Variant	rs877004
Chromosome Location	chr3:112527313-112527314
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11918030	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924727	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4682429	0.88[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes]
rs4682430	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56131252	0.86[ASN][1000 genomes]
rs56281019	0.89[ASN][1000 genomes]
rs58847501	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62263724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7614664	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7634413	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7637030	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9941979	0.91[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs877004	CD200R1	cis	multi-tissue	Pritchard

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112521000-112529800	Weak transcription	A549	lung
2	chr3:112521600-112531600	Weak transcription	Stomach Mucosa	stomach
3	chr3:112524400-112528600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr3:112524800-112528600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr3:112526000-112527600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:112526200-112527400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:112526200-112527600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:112526400-112527400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:112526600-112527600	Enhancers	Colon Smooth Muscle	Colon
10	chr3:112526600-112529400	Weak transcription	NHDF-Ad	bronchial
11	chr3:112526600-112530800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:112526800-112529200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:112526800-112529400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:112527000-112531000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:112527000-112531200	Weak transcription	Primary T cells from cord blood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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