Variant report

Variant	rs4664076
Chromosome Location	chr2:152921491-152921492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10190546	0.94[YRI][hapmap]
rs10930892	0.87[YRI][hapmap]
rs12465422	0.83[CHD][hapmap]
rs12474775	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12474991	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830598	0.82[CHB][hapmap]
rs16830616	0.87[CHB][hapmap];0.93[YRI][hapmap]
rs1949521	0.87[CHB][hapmap];0.81[YRI][hapmap]
rs2139417	0.87[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.93[YRI][hapmap]
rs2680982	0.96[ASN][1000 genomes]
rs2881059	0.82[CHB][hapmap]
rs3845845	0.82[CHB][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap]
rs4146376	0.87[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4664523	0.83[CHD][hapmap]
rs4664524	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs58147624	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58248711	0.82[ASN][1000 genomes]
rs58387407	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58761979	0.82[ASN][1000 genomes]
rs58975341	0.89[ASN][1000 genomes]
rs6433777	1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap]
rs6728019	1.00[CHB][hapmap]
rs6745978	0.83[CHD][hapmap]
rs6755776	0.82[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap]
rs7604835	0.87[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.89[MEX][hapmap]
rs7607695	0.82[CHB][hapmap]
rs9917218	0.80[CHB][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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4664076	C11orf17	trans	cerebellum	SCAN
rs4664076	STAM2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152916000-152932000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:152919400-152922600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:152920600-152924200	Weak transcription	A549	lung
4	chr2:152920800-152922000	Weak transcription	HSMMtube	muscle
5	chr2:152920800-152924800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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