Variant report

Variant	rs8085829
Chromosome Location	chr18:24537293-24537294
allele	G/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	TCF12	chr18:24536699-24537322	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr18:24536888-24537331	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr18:24536792-24537526	H1-neurons	neurons:	n/a	n/a
4	SP1	chr18:24536866-24537341	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr18:24536833-24537356	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr18:24536724-24537505	H1-neurons	neurons:	n/a	n/a
7	POU5F1	chr18:24536878-24537313	H1-hESC	embryonic stem cell:	n/a	chr18:24537072-24537086
8	SIN3A	chr18:24536830-24537332	H1-hESC	embryonic stem cell:	n/a	chr18:24536923-24536933
9	SP1	chr18:24536821-24537352	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTBP2	chr18:24536900-24537441	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr18:24536632-24537787	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000266549	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12326934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16943055	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16943181	0.88[EUR][1000 genomes]
rs28433105	0.88[EUR][1000 genomes]
rs3889349	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3889350	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55976171	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56403102	0.85[EUR][1000 genomes]
rs57465464	0.91[AMR][1000 genomes]
rs58569620	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60167332	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61089873	0.88[EUR][1000 genomes]
rs61998173	0.88[EUR][1000 genomes]
rs6508460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508463	0.88[EUR][1000 genomes]
rs67822335	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7227120	0.88[EUR][1000 genomes]
rs7232288	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7237212	0.88[EUR][1000 genomes]
rs7238255	0.88[EUR][1000 genomes]
rs7243196	0.91[AMR][1000 genomes]
rs72880575	0.85[EUR][1000 genomes]
rs8086337	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8088793	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8091201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9807634	0.91[AMR][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	nsv833600	chr18:24473894-24681019	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv909472	chr18:24479960-24614192	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1067103	chr18:24524011-24760469	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv543668	chr18:24524011-24760469	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:24536400-24537800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr18:24536600-24537400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:24536600-24537600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:24536600-24537600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr18:24536600-24538600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr18:24536800-24537400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:24536800-24537400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:24536800-24537400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr18:24536800-24537400	Enhancers	Brain Anterior Caudate	brain
10	chr18:24536800-24537400	Enhancers	Fetal Lung	lung
11	chr18:24536800-24537800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr18:24536800-24537800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:24536800-24538600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr18:24537000-24537400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr18:24537000-24537400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:24537000-24537400	Enhancers	Brain Angular Gyrus	brain
17	chr18:24537000-24537400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr18:24537000-24537400	Enhancers	Right Ventricle	heart
19	chr18:24537000-24537400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr18:24537000-24537800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr18:24537200-24537400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr18:24537200-24537400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr18:24537200-24537600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr18:24537200-24537800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr18:24537200-24537800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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