Variant report

Variant	rs2460560
Chromosome Location	chr10:43851057-43851058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43849709..43851969-chr10:43889837..43893145,4	MCF-7	breast:
2	chr10:43847068..43851484-chr10:43869685..43874039,8	MCF-7	breast:
3	chr10:43842333..43853034-chr10:43900806..43908178,21	MCF-7	breast:
4	chr10:43848751..43853953-chr10:43869065..43873618,8	MCF-7	breast:
5	chr10:43848373..43851166-chr10:43883249..43887179,4	MCF-7	breast:
6	chr10:43848475..43851407-chr10:43948589..43951104,3	MCF-7	breast:
7	chr10:43849658..43851212-chr10:43881372..43882946,2	MCF-7	breast:
8	chr10:43847403..43853479-chr10:43888233..43893881,11	MCF-7	breast:
9	chr10:43844606..43847679-chr10:43848074..43851632,6	MCF-7	breast:
10	chr10:43845683..43851518-chr10:43853877..43859694,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150201	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2090742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2249000	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2249001	0.87[AFR][1000 genomes]
rs2251787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2252458	1.00[AMR][1000 genomes]
rs2256073	1.00[AFR][1000 genomes]
rs2418930	1.00[AMR][1000 genomes]
rs2460564	1.00[AMR][1000 genomes]
rs2493662	1.00[AMR][1000 genomes]
rs2493664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58107178	1.00[EUR][1000 genomes]
rs7923134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43844400-43857200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:43846400-43852000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:43846600-43851200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr10:43846600-43851400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr10:43846600-43851600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr10:43846600-43857200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:43847000-43851200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:43848400-43851800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr10:43848600-43851400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr10:43848600-43851600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr10:43848600-43851800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr10:43848600-43852000	Enhancers	Brain Hippocampus Middle	brain
13	chr10:43848600-43852400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr10:43849000-43851400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr10:43849000-43857000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:43849200-43852000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr10:43849200-43852400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr10:43849200-43852600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:43849400-43851200	Enhancers	Hela-S3	cervix
20	chr10:43849400-43852400	Enhancers	NHEK	skin
21	chr10:43849400-43852600	Enhancers	K562	blood
22	chr10:43849600-43851600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:43849800-43851200	Enhancers	A549	lung
24	chr10:43850000-43851200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr10:43850000-43851200	Weak transcription	HSMMtube	muscle
26	chr10:43850000-43851400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:43850000-43851600	Weak transcription	Fetal Intestine Large	intestine
28	chr10:43850000-43851600	Weak transcription	Pancreas	Pancrea
29	chr10:43850000-43851800	Weak transcription	Fetal Intestine Small	intestine
30	chr10:43850000-43857000	Weak transcription	Brain Angular Gyrus	brain
31	chr10:43850000-43857000	Weak transcription	Brain Anterior Caudate	brain
32	chr10:43850000-43857000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr10:43850200-43851200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:43850200-43851200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:43850400-43852400	Enhancers	HMEC	breast
36	chr10:43850600-43851200	Weak transcription	Stomach Mucosa	stomach
37	chr10:43850600-43852400	Weak transcription	Fetal Kidney	kidney
38	chr10:43850800-43851200	Weak transcription	Brain Substantia Nigra	brain
39	chr10:43850800-43851600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr10:43850800-43852000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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