Variant report

Variant	rs6455294
Chromosome Location	chr6:69343489-69343490
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	RAD21	chr6:69342384-69347457	SK-N-SH	brain:	n/a	chr6:69345907-69345917 chr6:69345020-69345034 chr6:69344689-69344699 chr6:69343839-69343849 chr6:69345328-69345338
2	RFX5	chr6:69342558-69347581	SK-N-SH	brain:	n/a	chr6:69344290-69344305 chr6:69346927-69346936 chr6:69344290-69344305
3	REST	chr6:69343340-69345936	H1-neurons	neurons:	n/a	n/a
4	STAT3	chr6:69343372-69343572	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL713998.1-2	chr6:69342555-69344919	ENSG00000230910.2

Variant related genes	Relation type
BAI3	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs16880686	1.00[EUR][1000 genomes]
rs16900133	1.00[AMR][1000 genomes]
rs16900145	1.00[AMR][1000 genomes]
rs59854565	1.00[EUR][1000 genomes]
rs6455293	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6905504	1.00[EUR][1000 genomes]
rs73745883	1.00[EUR][1000 genomes]
rs73745884	1.00[EUR][1000 genomes]
rs7759211	1.00[AMR][1000 genomes]
rs9454590	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv830680	chr6:69192214-69351103	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69342600-69343600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:69342600-69343600	Enhancers	Brain Substantia Nigra	brain
3	chr6:69342600-69343600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr6:69342600-69343800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:69342600-69349600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:69342600-69351000	Active TSS	Brain Angular Gyrus	brain
7	chr6:69342800-69343600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:69342800-69343800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr6:69342800-69344200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr6:69342800-69348000	Active TSS	Fetal Brain Male	brain
11	chr6:69343000-69344000	Weak transcription	Psoas Muscle	Psoas
12	chr6:69343000-69348000	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr6:69343200-69343600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr6:69343200-69343600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr6:69343200-69343600	Weak transcription	K562	blood
16	chr6:69343200-69344200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:69343200-69344400	Bivalent/Poised TSS	Fetal Lung	lung
18	chr6:69343200-69348600	Active TSS	Brain Cingulate Gyrus	brain
19	chr6:69343200-69348800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:69343200-69349200	Active TSS	Brain Germinal Matrix	brain
21	chr6:69343200-69351200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr6:69343200-69352000	Active TSS	Brain Anterior Caudate	brain
23	chr6:69343400-69343600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:69343400-69343600	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr6:69343400-69343800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr6:69343400-69344000	Active TSS	Stomach Smooth Muscle	stomach
27	chr6:69343400-69348400	Active TSS	Fetal Stomach	stomach
28	chr6:69343400-69349600	Active TSS	Fetal Brain Female	brain

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