Variant report

Variant	rs16854003
Chromosome Location	chr1:179336996-179336997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
2	chr1:179049954..179052769-chr1:179333565..179337813,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186283	Chromatin interaction
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10913736	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577489	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11581507	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11799784	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11804234	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13306727	0.80[EUR][1000 genomes]
rs13306730	0.80[EUR][1000 genomes]
rs16853998	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17369088	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2184575	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs45471092	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4652366	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55906130	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55986478	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149964	0.81[ASN][1000 genomes]
rs56303406	0.81[ASN][1000 genomes]
rs57864135	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682068	0.86[EUR][1000 genomes]
rs67545145	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68098532	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7534976	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16854003	AXDND1	cis	Thyroid	GTEx
rs16854003	TDRD5	cis	Artery Aorta	GTEx
rs16854003	AXDND1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179336000-179338400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:179336800-179337200	Enhancers	HepG2	liver

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