Variant report

Variant	rs17180771
Chromosome Location	chr3:19975139-19975140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr3:19975092-19975969	K562	blood:	n/a	n/a
2	CTCF	chr3:19975000-19975150	GM12869	blood:	n/a	n/a
3	RCOR1	chr3:19972538-19976115	K562	blood:	n/a	n/a
4	UBTF	chr3:19975046-19975949	K562	blood:	n/a	n/a

Variant related genes	Relation type
EFHB	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10155054	0.91[ASN][1000 genomes]
rs10510497	0.80[CEU][hapmap]
rs11927871	0.91[ASN][1000 genomes]
rs12374092	1.00[AFR][1000 genomes]
rs12486167	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap]
rs12486526	0.80[CEU][hapmap]
rs12490848	1.00[AFR][1000 genomes]
rs13097409	1.00[LWK][hapmap]
rs17574049	0.91[ASN][1000 genomes]
rs17796230	0.80[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap]
rs1872737	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2101390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28597881	1.00[AFR][1000 genomes]
rs3849533	1.00[CEU][hapmap];1.00[CHB][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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916092	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4241539	0.80[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap]
rs4618239	1.00[AFR][1000 genomes]
rs4858674	1.00[AFR][1000 genomes]
rs4858712	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4858713	0.91[ASN][1000 genomes]
rs4858714	0.91[ASN][1000 genomes]
rs4858768	1.00[LWK][hapmap]
rs55669125	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797296	1.00[AFR][1000 genomes]
rs55829813	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55892327	1.00[AFR][1000 genomes]
rs56004950	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59572420	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62241326	1.00[AFR][1000 genomes]
rs62241330	1.00[AFR][1000 genomes]
rs62241334	1.00[AFR][1000 genomes]
rs62279119	0.91[ASN][1000 genomes]
rs62279120	0.91[ASN][1000 genomes]
rs62279122	0.91[ASN][1000 genomes]
rs62279123	0.91[ASN][1000 genomes]
rs62279125	0.91[ASN][1000 genomes]
rs62279132	0.91[ASN][1000 genomes]
rs62279133	0.91[ASN][1000 genomes]
rs62279134	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62279135	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62279136	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62279138	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6550213	0.91[ASN][1000 genomes]
rs66526230	0.91[ASN][1000 genomes]
rs73046020	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9809548	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9810613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17180771	EFHB	cis	Muscle Skeletal	GTEx
rs17180771	EFHB	cis	lung	GTEx
rs17180771	EFHB	cis	cerebellum	SCAN
rs17180771	EFHB	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19973000-19975400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:19973600-19975400	Enhancers	Primary hematopoietic stem cells	blood
3	chr3:19973600-19979200	Weak transcription	HMEC	breast
4	chr3:19973600-19987200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:19973800-19975400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:19973800-19978400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:19973800-19979000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:19974000-19975400	Weak transcription	A549	lung
9	chr3:19974000-19975400	Enhancers	K562	blood
10	chr3:19974200-19979200	Weak transcription	Hela-S3	cervix
11	chr3:19974600-19976000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:19974800-19975800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:19975000-19975200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:19975000-19975400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr3:19975000-19975400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:19975000-19975600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:19975000-19976000	Enhancers	HepG2	liver
18	chr3:19975000-19976400	Active TSS	iPS-15b Cell Line	embryonic stem cell

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