Variant report

Variant	rs13062528
Chromosome Location	chr3:42856350-42856351
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	EP300	chr3:42856327-42856615	HepG2	liver:	n/a	chr3:42856503-42856513
2	FOSL2	chr3:42856341-42856706	HepG2	liver:	n/a	chr3:42856550-42856560 chr3:42856550-42856560 chr3:42856550-42856560
3	FOXA1	chr3:42856289-42856726	HepG2	liver:	n/a	n/a
4	KAP1	chr3:42856326-42857806	U2OS	brain:	n/a	n/a
5	FOXA1	chr3:42856350-42856770	HepG2	liver:	n/a	n/a
6	KAP1	chr3:42856175-42857851	HEK293	kidney:	n/a	n/a
7	FOXA1	chr3:42856275-42856721	HepG2	liver:	n/a	n/a
8	ZNF263	chr3:42856276-42857439	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42842006..42848504-chr3:42854036..42858354,7	K562	blood:
2	chr3:42846757..42848695-chr3:42854131..42856830,2	K562	blood:
3	chr3:42841845..42845236-chr3:42855285..42858253,3	K562	blood:
4	chr3:42853502..42856729-chr3:42859080..42861862,4	MCF-7	breast:

Variant related genes	Relation type
ACKR2	TF binding region
ENSG00000144648	Chromatin interaction
ENSG00000181061	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11129971	0.84[AFR][1000 genomes]
rs11129973	0.84[ASW][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap]
rs11708224	0.84[AFR][1000 genomes]
rs11720829	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs12488173	0.84[AFR][1000 genomes]
rs1991438	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs339663	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs339669	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs339673	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs339675	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs339679	0.95[YRI][hapmap]
rs4399859	0.85[AFR][1000 genomes]
rs4404423	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4682855	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs4683334	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5027058	0.85[AFR][1000 genomes]
rs6442065	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs6773636	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs6778695	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6787667	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs7610350	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes]
rs7612614	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs7612782	0.91[AFR][1000 genomes]
rs7634974	0.85[AMR][1000 genomes]
rs7648688	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.82[AFR][1000 genomes]
rs9755640	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs9866005	0.88[YRI][hapmap];0.81[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1847016	chr3:42855765-42880490	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42846800-42856400	Weak transcription	Right Atrium	heart
2	chr3:42847200-42856400	Weak transcription	NHEK	skin
3	chr3:42849800-42856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:42853200-42856600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:42853200-42858600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr3:42853600-42856400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:42853800-42856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:42853800-42861000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:42853800-42861200	Weak transcription	Fetal Intestine Large	intestine
10	chr3:42853800-42862200	Weak transcription	Fetal Intestine Small	intestine
11	chr3:42854000-42856600	Weak transcription	Fetal Kidney	kidney
12	chr3:42854200-42861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:42854800-42858000	Enhancers	Fetal Heart	heart
14	chr3:42855000-42857600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr3:42855600-42856400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr3:42855600-42857400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr3:42855800-42857400	Enhancers	K562	blood
18	chr3:42855800-42857800	Enhancers	HepG2	liver
19	chr3:42856000-42856800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:42856000-42857200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:42856000-42857600	Enhancers	Stomach Mucosa	stomach
22	chr3:42856000-42857800	Enhancers	Hela-S3	cervix
23	chr3:42856200-42856400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:42856200-42856400	Enhancers	Colonic Mucosa	Colon
25	chr3:42856200-42857000	Enhancers	Placenta	Placenta
26	chr3:42856200-42857200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:42856200-42857400	Enhancers	Stomach Smooth Muscle	stomach
28	chr3:42856200-42857400	Enhancers	HMEC	breast
29	chr3:42856200-42858000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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