Variant report

Variant	rs6458438
Chromosome Location	chr6:12750721-12750722
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	NRF1	chr6:12750102-12750742	SK-N-SH	brain:	n/a	chr6:12750337-12750346 chr6:12750474-12750483 chr6:12750339-12750348
2	SIN3A	chr6:12748563-12750726	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr6:12748447-12750926	SK-N-SH	brain:	n/a	n/a
4	ZNF263	chr6:12750214-12751019	HEK293-T-REx	kidney:	n/a	chr6:12750257-12750266
5	POLR2A	chr6:12749194-12750748	H1-neurons	neurons:	n/a	n/a
6	REST	chr6:12748947-12751024	H1-neurons	neurons:	n/a	chr6:12750584-12750604 chr6:12750905-12750923 chr6:12750584-12750604 chr6:12750914-12750932
7	POLR2A	chr6:12749773-12750735	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000223291	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs510620	0.81[EUR][1000 genomes]
rs522117	0.81[EUR][1000 genomes]
rs56793208	0.91[ASN][1000 genomes]
rs6458439	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs868483	0.84[EUR][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	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3361165	chr6:12748791-12751339	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
4	esv3432117	chr6:12748916-12751314	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12748800-12751000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:12748800-12752600	Active TSS	Fetal Brain Female	brain
3	chr6:12749000-12750800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:12749000-12751000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:12749000-12751000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:12749200-12751000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:12749400-12750800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:12749600-12751000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:12749800-12750800	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:12750000-12750800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:12750200-12750800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:12750200-12751000	Active TSS	Gastric	stomach
13	chr6:12750400-12750800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:12750400-12750800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:12750400-12751000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:12750400-12751000	Bivalent Enhancer	Brain Anterior Caudate	brain
17	chr6:12750400-12751600	Flanking Active TSS	Fetal Brain Male	brain
18	chr6:12750600-12750800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr6:12750600-12750800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr6:12750600-12750800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:12750600-12750800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:12750600-12750800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr6:12750600-12750800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:12750600-12750800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:12750600-12750800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
26	chr6:12750600-12750800	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
27	chr6:12750600-12750800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
28	chr6:12750600-12750800	Flanking Active TSS	HSMM	muscle
29	chr6:12750600-12751000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr6:12750600-12751600	Flanking Active TSS	Brain Germinal Matrix	brain

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