Variant report

Variant	rs2294344
Chromosome Location	chr6:25652225-25652226
allele	A/C
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	REST	chr6:25652070-25653103	MCF-7	breast:	n/a	chr6:25652472-25652485
2	REST	chr6:25652042-25653095	ECC-1	luminal epithelium:	n/a	chr6:25652472-25652485
3	REST	chr6:25652135-25652920	HL-60	blood:	n/a	chr6:25652472-25652485
4	REST	chr6:25652079-25653101	ECC-1	luminal epithelium:	n/a	chr6:25652472-25652485
5	REST	chr6:25651999-25652950	PFSK-1	brain:	n/a	chr6:25652472-25652485
6	REST	chr6:25651986-25653222	HL-60	blood:	n/a	chr6:25652472-25652485
7	REST	chr6:25652178-25653112	PANC-1	pancreas:	n/a	chr6:25652472-25652485
8	REST	chr6:25652138-25652950	GM12878	blood:	n/a	chr6:25652472-25652485
9	REST	chr6:25652186-25653011	MCF-7	breast:	n/a	chr6:25652472-25652485
10	REST	chr6:25652194-25653105	H1-neurons	neurons:	n/a	chr6:25652472-25652485
11	REST	chr6:25652167-25652827	H1-hESC	embryonic stem cell:	n/a	chr6:25652472-25652485
12	REST	chr6:25652206-25652894	HepG2	liver:	n/a	chr6:25652472-25652485
13	REST	chr6:25652073-25652904	K562	blood:	n/a	chr6:25652472-25652485
14	RAD21	chr6:25652172-25652859	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr6:25652060-25652924	SK-N-SH	brain:	n/a	chr6:25652472-25652485
16	REST	chr6:25652173-25652811	K562	blood:	n/a	chr6:25652472-25652485
17	REST	chr6:25652185-25652911	H1-hESC	embryonic stem cell:	n/a	chr6:25652472-25652485
18	REST	chr6:25652217-25653051	HCT-116	colon:	n/a	chr6:25652472-25652485
19	REST	chr6:25652105-25653093	A549	lung:	n/a	chr6:25652472-25652485
20	REST	chr6:25651987-25653066	PFSK-1	brain:	n/a	chr6:25652472-25652485
21	SIN3A	chr6:25652143-25652846	H1-hESC	embryonic stem cell:	n/a	chr6:25652472-25652485
22	REST	chr6:25651994-25653163	HepG2	liver:	n/a	chr6:25652472-25652485
23	REST	chr6:25651990-25653001	HepG2	liver:	n/a	chr6:25652472-25652485

Variant related genes	Relation type
SCGN	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028319	1.00[AFR][1000 genomes]
rs10498728	1.00[YRI][hapmap]
rs11969981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524760	0.82[GIH][hapmap]
rs12526321	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12528159	1.00[AFR][1000 genomes]
rs17252870	1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17253044	1.00[JPT][hapmap]
rs17270561	1.00[LWK][hapmap]
rs17322552	1.00[YRI][hapmap]
rs17491869	1.00[AFR][1000 genomes]
rs2064128	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs214055	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs301393	1.00[JPT][hapmap]
rs35676593	1.00[AFR][1000 genomes]
rs3788994	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3804133	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3923725	1.00[YRI][hapmap]
rs4140641	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419666	1.00[YRI][hapmap]
rs4712950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712953	0.84[GIH][hapmap]
rs57141743	1.00[AFR][1000 genomes]
rs60626645	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61340952	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
4	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2294344	ZSCAN23	cis	parietal	SCAN
rs2294344	KAAG1	cis	parietal	SCAN
rs2294344	HIST1H2AJ	cis	parietal	SCAN
rs2294344	HIST1H4L	cis	parietal	SCAN
rs2294344	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25651800-25652600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
2	chr6:25651800-25652800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:25652000-25652400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
4	chr6:25652000-25652400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
5	chr6:25652000-25652400	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr6:25652000-25652600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:25652000-25652600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:25652000-25652600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:25652000-25652600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:25652000-25652600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:25652000-25652800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:25652000-25652800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
13	chr6:25652000-25653000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr6:25652200-25652400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:25652200-25652400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:25652200-25652400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:25652200-25652400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:25652200-25652400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:25652200-25652400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:25652200-25652400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:25652200-25652400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr6:25652200-25652400	Bivalent Enhancer	Brain Hippocampus Middle	brain
23	chr6:25652200-25652400	Bivalent Enhancer	Brain Substantia Nigra	brain
24	chr6:25652200-25652400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr6:25652200-25652400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
26	chr6:25652200-25652400	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr6:25652200-25652400	Bivalent Enhancer	HSMM	muscle
28	chr6:25652200-25652600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr6:25652200-25652600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:25652200-25652600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:25652200-25652600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:25652200-25652600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:25652200-25652600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:25652200-25652600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:25652200-25652600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:25652200-25652600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:25652200-25652600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:25652200-25652600	Bivalent Enhancer	Fetal Stomach	stomach
39	chr6:25652200-25652600	Bivalent Enhancer	Lung	lung
40	chr6:25652200-25652600	Enhancers	Ovary	ovary
41	chr6:25652200-25652600	Bivalent/Poised TSS	NHEK	skin
42	chr6:25652200-25652800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:25652200-25652800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:25652200-25652800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr6:25652200-25652800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr6:25652200-25652800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:25652200-25652800	Bivalent Enhancer	Esophagus	oesophagus
48	chr6:25652200-25652800	Bivalent Enhancer	Fetal Brain Male	brain
49	chr6:25652200-25652800	Enhancers	Fetal Muscle Trunk	muscle
50	chr6:25652200-25652800	Enhancers	Gastric	stomach

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