Variant report

Variant	rs6531840
Chromosome Location	chr4:86525223-86525224
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	CREB1	chr4:86525121-86525407	GM12878	blood:	n/a	chr4:86525247-86525260
2	ATF2	chr4:86524538-86525240	GM12878	blood:	n/a	n/a
3	GATA3	chr4:86524782-86525549	SH-SY5Y	brain:	n/a	n/a
4	EP300	chr4:86525145-86525488	SK-N-SH_RA	brain:	n/a	chr4:86525278-86525287
5	EP300	chr4:86524743-86525445	SK-N-SH_RA	brain:	n/a	chr4:86525278-86525287
6	EP300	chr4:86524274-86525741	SK-N-SH	brain:	n/a	chr4:86525278-86525287
7	GATA2	chr4:86524931-86525541	SH-SY5Y	brain:	n/a	n/a
8	CREB1	chr4:86524667-86525267	GM12878	blood:	n/a	chr4:86525247-86525260
9	ATF1	chr4:86525152-86525363	K562	blood:	n/a	n/a

Variant related genes	Relation type
ARHGAP24	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs28429534	1.00[AMR][1000 genomes]
rs28871342	1.00[AMR][1000 genomes]
rs6813231	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6814544	0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6815200	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs6816066	1.00[AMR][1000 genomes]
rs6827386	1.00[AMR][1000 genomes]
rs6827564	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6858619	1.00[AMR][1000 genomes]
rs6858779	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7654408	1.00[AMR][1000 genomes]
rs7657112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7657712	1.00[ASW][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs7662585	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs7667098	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671828	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs7672626	1.00[AMR][1000 genomes]
rs7672782	1.00[ASW][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7673815	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7685260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7685271	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs7688778	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7689198	1.00[AMR][1000 genomes]
rs7689606	1.00[AMR][1000 genomes]
rs7690114	1.00[AMR][1000 genomes]
rs7690209	1.00[AMR][1000 genomes]

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	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv829999	chr4:86500257-86666019	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86517800-86542200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:86523800-86526200	Enhancers	Primary B cells from peripheral blood	blood
3	chr4:86524400-86525400	Enhancers	GM12878-XiMat	blood
4	chr4:86524800-86525400	Weak transcription	Primary B cells from cord blood	blood
5	chr4:86524800-86525400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:86524800-86525400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:86524800-86525400	Enhancers	Brain Cingulate Gyrus	brain
8	chr4:86524800-86525800	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr4:86525000-86525400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:86525000-86525400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:86525000-86525400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:86525000-86525400	Enhancers	Brain Angular Gyrus	brain
13	chr4:86525000-86525400	Enhancers	Brain Anterior Caudate	brain
14	chr4:86525000-86525400	Enhancers	Brain Hippocampus Middle	brain
15	chr4:86525000-86525400	Enhancers	Fetal Kidney	kidney
16	chr4:86525000-86525600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:86525200-86525400	Enhancers	Gastric	stomach
18	chr4:86525200-86525400	Enhancers	Left Ventricle	heart
19	chr4:86525200-86525400	Enhancers	Stomach Mucosa	stomach
20	chr4:86525200-86525400	Enhancers	HUVEC	blood vessel
21	chr4:86525200-86525600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:86525200-86525600	Genic enhancers	HSMM	muscle

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