Variant report

Variant	rs998672
Chromosome Location	chr1:146504878-146504879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10218707	0.80[CHB][hapmap]
rs10900384	0.88[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap]
rs11240094	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs12122453	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs12122534	0.94[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12123494	0.86[ASN][1000 genomes]
rs12141387	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs12742988	0.90[CHB][hapmap]
rs1925343	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs1984615	0.96[YRI][hapmap]
rs2031481	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs3851279	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3862921	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4950332	0.90[CHB][hapmap]
rs517201	0.90[CHB][hapmap]
rs524016	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs604716	0.90[CHB][hapmap]
rs614763	0.90[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428224	chr1:145613243-146553918	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS 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	95 gene(s)	inside rSNPs	diseases
4	nsv946295	chr1:146471863-146507583	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
6	nsv872253	chr1:146494246-146548549	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv872254	chr1:146503841-146544721	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs998672	RP11-94I2.1	cis	lung	GTEx
rs998672	RP11-325P15.1	cis	lung	GTEx
rs998672	NBPF13P	cis	lung	GTEx
rs998672	GNRHR2	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146501600-146506800	Weak transcription	NHEK	skin
2	chr1:146504600-146508800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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