Variant report

Variant	rs2476598
Chromosome Location	chr1:114468256-114468257
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000134262	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1000528	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217441	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147079	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4381184	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6658209	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702833	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7522987	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7545038	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551215	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7554371	0.87[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2476598	OLFML3	cis	Esophagus Muscularis	GTEx
rs2476598	NGF	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114449800-114470400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:114456200-114470400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:114456200-114470600	Weak transcription	Brain Substantia Nigra	brain
4	chr1:114456200-114471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:114456400-114470400	Weak transcription	HSMM	muscle
6	chr1:114457200-114470600	Weak transcription	Primary T cells from cord blood	blood
7	chr1:114457600-114470400	Weak transcription	Fetal Thymus	thymus
8	chr1:114459200-114470400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:114467000-114470400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:114467200-114470400	Weak transcription	Primary monocytes fromperipheralblood	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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