Variant report

Variant	rs62154952
Chromosome Location	chr2:67620199-67620200
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	POLR2A	chr2:67620050-67620234	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:67618460..67620828-chr2:67621432..67622983,2	MCF-7	breast:
2	chr2:67616796..67619602-chr2:67619811..67621900,2	K562	blood:
3	chr2:67618650..67620749-chr2:67623757..67625707,2	K562	blood:
4	chr2:67608824..67611674-chr2:67618385..67620803,2	MCF-7	breast:
5	chr2:67618556..67622111-chr2:67623291..67626187,3	MCF-7	breast:

Variant related genes	Relation type
ETAA1	TF binding region
ENSG00000143971	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10496153	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1063571	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12185591	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12185702	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12988210	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12991090	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12996359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000557	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004747	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004765	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13009070	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13015319	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13015349	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13016330	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13016336	0.86[EUR][1000 genomes]
rs13017696	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13018272	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13018894	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13026513	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13030037	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13030211	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13034744	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13035051	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13035754	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13036061	0.87[EUR][1000 genomes]
rs1384743	0.83[AFR][1000 genomes]
rs1384744	0.83[AFR][1000 genomes]
rs1521051	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17544516	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17544551	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17545245	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17545301	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17545329	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17603029	0.83[AFR][1000 genomes]
rs17603914	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2171176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2861645	0.83[AFR][1000 genomes]
rs2902008	0.83[AFR][1000 genomes]
rs34103917	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34274370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34281542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34298852	0.88[AMR][1000 genomes]
rs34418651	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34493710	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34547630	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34636997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34737312	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34920978	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34962808	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34997300	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35002490	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35141978	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35144434	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35340993	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35382600	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35503819	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35570926	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35593975	0.84[EUR][1000 genomes]
rs35607813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35610403	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35686078	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35777125	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36098430	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4428006	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4671806	0.83[AFR][1000 genomes]
rs62154898	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62154948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62154955	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154957	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62154958	0.88[EUR][1000 genomes]
rs62156538	0.83[AFR][1000 genomes]
rs62156540	0.83[AFR][1000 genomes]
rs62156541	0.83[AFR][1000 genomes]
rs62156688	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62156689	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156692	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156693	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62156695	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156696	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62156698	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62156699	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156700	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156702	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156703	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156754	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62156756	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156757	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156758	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62158282	0.83[AFR][1000 genomes]
rs62158289	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62158290	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6710099	0.86[EUR][1000 genomes]
rs6725762	0.84[EUR][1000 genomes]
rs71411986	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71411987	0.88[AMR][1000 genomes]
rs71411988	0.88[AMR][1000 genomes]
rs7585807	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008584	chr2:67168244-67703601	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535775	chr2:67168244-67703601	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv834249	chr2:67515471-67691605	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3335541	chr2:67577544-67773907	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67606600-67624200	Weak transcription	Pancreas	Pancrea
2	chr2:67613200-67621600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:67617200-67620600	Weak transcription	NHEK	skin
4	chr2:67617200-67621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:67617200-67621400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:67617200-67621600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:67617200-67622200	Weak transcription	HMEC	breast
8	chr2:67617400-67620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:67617400-67620200	Weak transcription	NH-A	brain
10	chr2:67617400-67621200	Weak transcription	Hela-S3	cervix
11	chr2:67617400-67624200	Weak transcription	Aorta	Aorta
12	chr2:67617600-67620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:67617600-67624000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:67617800-67620200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:67617800-67620200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:67617800-67620200	Weak transcription	HUVEC	blood vessel
17	chr2:67617800-67621600	Weak transcription	HSMM	muscle
18	chr2:67617800-67621800	Weak transcription	HSMMtube	muscle
19	chr2:67618000-67621200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:67618600-67622000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:67618600-67624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:67618800-67622200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:67618800-67624000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:67619600-67620400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:67619600-67620400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:67619600-67620400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:67619600-67621800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:67619600-67622000	Enhancers	NHLF	lung
29	chr2:67619600-67622600	Enhancers	NHDF-Ad	bronchial
30	chr2:67619600-67622600	Enhancers	Osteobl	bone
31	chr2:67619800-67620200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:67619800-67620400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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