Variant report

Variant	rs17654071
Chromosome Location	chr1:154369252-154369253
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	chr1:154367430..154370038-chr1:154375786..154377764,2	MCF-7	breast:
2	chr1:154360935..154363214-chr1:154367136..154369854,2	K562	blood:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10908831	0.81[AMR][1000 genomes]
rs10908835	0.80[CHD][hapmap]
rs11265604	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1194584	0.85[CHD][hapmap];0.84[GIH][hapmap]
rs1194585	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs1194586	0.81[GIH][hapmap]
rs1194587	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs1194607	0.90[CHD][hapmap];0.84[GIH][hapmap]
rs12029292	0.88[AMR][1000 genomes]
rs12033720	0.88[CHD][hapmap]
rs12121085	0.93[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12127600	0.80[CHD][hapmap]
rs1760794	0.86[CHD][hapmap];0.84[GIH][hapmap]
rs4075015	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4845612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427627	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs6692515	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72696290	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72698103	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514026	0.80[AMR][1000 genomes]
rs952146	0.80[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17654071	EFNA3	cis	parietal	SCAN
rs17654071	THEM4	cis	parietal	SCAN
rs17654071	LCE2D	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154360400-154370000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:154364400-154377200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:154367200-154374200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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