Variant report

Variant	rs72925433
Chromosome Location	chr2:39360701-39360702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:39360237-39360776	HepG2	liver:	n/a	n/a
2	ARID3A	chr2:39360488-39360731	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39358031..39362725-chr2:39365919..39368876,6	K562	blood:
2	chr2:39351946..39354916-chr2:39358761..39361361,2	K562	blood:
3	chr2:39351119..39353024-chr2:39359111..39360960,2	K562	blood:
4	chr2:39346601..39349428-chr2:39359209..39363502,5	MCF-7	breast:
5	chr2:39357363..39365432-chr2:39365480..39370907,10	K562	blood:
6	chr2:39347065..39349940-chr2:39360622..39363003,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202309	TF binding region
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10184046	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10184855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186842	1.00[EUR][1000 genomes]
rs10188701	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10189440	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10196863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10199955	1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10203565	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207187	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10207984	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13394446	1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13411756	1.00[EUR][1000 genomes]
rs13414685	1.00[EUR][1000 genomes]
rs13416725	1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs13425165	1.00[EUR][1000 genomes]
rs13428418	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13432395	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17023214	1.00[EUR][1000 genomes]
rs17023241	1.00[EUR][1000 genomes]
rs17023292	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55890805	1.00[EUR][1000 genomes]
rs56269328	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56724744	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57359008	1.00[EUR][1000 genomes]
rs59259697	1.00[EUR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61596046	1.00[EUR][1000 genomes]
rs6544200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6734212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737680	1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs72925431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925439	1.00[EUR][1000 genomes]
rs7340303	1.00[EUR][1000 genomes]
rs73930506	1.00[EUR][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7564481	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7565814	1.00[EUR][1000 genomes]
rs7571608	1.00[EUR][1000 genomes]
rs7571719	1.00[EUR][1000 genomes]
rs7574214	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7582586	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7589303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599990	1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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	35 gene(s)	inside rSNPs	diseases
9	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39352800-39362800	Weak transcription	Thymus	Thymus
2	chr2:39352800-39368600	Weak transcription	HMEC	breast
3	chr2:39355400-39366000	Weak transcription	Hela-S3	cervix
4	chr2:39356800-39361200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:39356800-39361400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:39356800-39362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:39357200-39362600	Weak transcription	Dnd41	blood
8	chr2:39357400-39362800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:39357600-39362600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:39357600-39362800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr2:39357800-39362600	Weak transcription	Fetal Thymus	thymus
12	chr2:39358400-39361000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:39358400-39362600	Weak transcription	Primary T cells from cord blood	blood
14	chr2:39358400-39362600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:39358400-39362800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:39358600-39362600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:39358600-39362800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:39359600-39362800	Weak transcription	K562	blood
19	chr2:39360000-39360800	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:39360000-39360800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:39360400-39360800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:39360400-39361200	Enhancers	HepG2	liver
23	chr2:39360400-39362000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr2:39360400-39362200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:39360400-39362800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:39360600-39362800	Weak transcription	Primary B cells from cord blood	blood
27	chr2:39360600-39366800	Weak transcription	Primary monocytes fromperipheralblood	blood

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