Variant report

Variant	rs2523856
Chromosome Location	chr6:31021630-31021631
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	PBX3	chr6:31021610-31022165	SK-N-SH	brain:	n/a	chr6:31021905-31021914

Variant related genes	Relation type
HCG22	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2251825	0.90[ASN][1000 genomes]
rs2252195	0.90[ASN][1000 genomes]
rs2256436	0.81[ASN][1000 genomes]
rs2394424	0.90[ASN][1000 genomes]
rs2428516	0.84[ASN][1000 genomes]
rs2517500	0.81[ASN][1000 genomes]
rs2517502	0.81[ASN][1000 genomes]
rs2517507	0.81[ASN][1000 genomes]
rs2517510	0.81[ASN][1000 genomes]
rs2517511	0.81[ASN][1000 genomes]
rs2517513	0.81[ASN][1000 genomes]
rs2517516	0.81[ASN][1000 genomes]
rs2517523	0.81[ASN][1000 genomes]
rs2517524	0.85[AMR][1000 genomes]
rs2517525	0.81[ASN][1000 genomes]
rs2517527	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2517532	0.90[ASN][1000 genomes]
rs2517533	0.90[ASN][1000 genomes]
rs2517534	0.87[ASN][1000 genomes]
rs2517538	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2517552	0.80[EUR][1000 genomes]
rs2523838	0.80[ASN][1000 genomes]
rs2523846	0.81[ASN][1000 genomes]
rs2523852	0.81[ASN][1000 genomes]
rs2523854	0.81[ASN][1000 genomes]
rs2523857	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2523858	0.90[ASN][1000 genomes]
rs2523862	0.90[ASN][1000 genomes]
rs2523870	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2523872	0.81[EUR][1000 genomes]
rs3131789	0.88[ASN][1000 genomes]
rs3132562	0.81[AMR][1000 genomes]
rs9262628	0.81[ASN][1000 genomes]
rs9262629	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884130	chr6:31014305-31038756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv884131	chr6:31014305-31040725	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv970677	chr6:31020994-31026537	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3370627	chr6:31021373-31025571	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2523856	TCF19	Cis_1M	lymphoblastoid	RTeQTL
rs2523856	HCG22	cis	Lymphoblastoid	GTEx
rs2523856	hmm31752	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31009600-31027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:31020800-31022200	Enhancers	Fetal Heart	heart
3	chr6:31020800-31022400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr6:31020800-31022400	ZNF genes & repeats	GM12878-XiMat	blood
5	chr6:31021200-31022000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:31021200-31022200	Bivalent Enhancer	Fetal Stomach	stomach
7	chr6:31021400-31022000	Enhancers	Fetal Brain Male	brain
8	chr6:31021400-31022200	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:31021400-31022200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:31021600-31021800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:31021600-31021800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:31021600-31021800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:31021600-31021800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:31021600-31021800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:31021600-31021800	Enhancers	Fetal Lung	lung
16	chr6:31021600-31021800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
17	chr6:31021600-31021800	Bivalent Enhancer	Fetal Thymus	thymus
18	chr6:31021600-31022000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:31021600-31022000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:31021600-31022000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:31021600-31022000	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr6:31021600-31022000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
23	chr6:31021600-31022200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:31021600-31022200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:31021600-31022200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr6:31021600-31022200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:31021600-31022200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:31021600-31022400	Active TSS	Brain Anterior Caudate	brain

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