Variant report

Variant	rs1401401
Chromosome Location	chr4:165927956-165927957
allele	A/G
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	YY1	chr4:165927706-165927959	H1-hESC	embryonic stem cell:	n/a	n/a
2	EGR1	chr4:165927507-165927994	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr4:165927740-165927961	K562	blood:	n/a	n/a
4	USF1	chr4:165927463-165927973	ECC-1	luminal epithelium:	n/a	n/a
5	EGR1	chr4:165927569-165928011	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr4:165927685-165928048	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr4:165927440-165927962	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr4:165927383-165928016	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000250712	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11100583	0.82[CEU][hapmap];0.85[AMR][1000 genomes]
rs12507869	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12510464	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12512234	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12647419	0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12647427	0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13110309	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13120990	0.82[CEU][hapmap]
rs13134940	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13137799	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13141887	0.80[EUR][1000 genomes]
rs13144590	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13151290	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13151735	0.86[EUR][1000 genomes]
rs1401399	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1401400	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17623445	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2056252	0.80[EUR][1000 genomes]
rs2176634	0.87[EUR][1000 genomes]
rs2280325	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280327	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35449092	0.80[EUR][1000 genomes]
rs3733418	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3733419	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4690797	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4691138	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71641138	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72697952	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7656863	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7657444	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7657639	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8180162	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165925800-165929000	Weak transcription	Fetal Brain Male	brain
2	chr4:165927000-165930000	Weak transcription	Right Atrium	heart
3	chr4:165927600-165928000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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