Variant report

Variant	rs10466239
Chromosome Location	chr10:43849827-43849828
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 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	chr10:43847924..43850753-chr10:43885592..43887337,2	MCF-7	breast:
5	chr10:43848751..43853953-chr10:43869065..43873618,8	MCF-7	breast:
6	chr10:43848373..43851166-chr10:43883249..43887179,4	MCF-7	breast:
7	chr10:43848475..43851407-chr10:43948589..43951104,3	MCF-7	breast:
8	chr10:43849658..43851212-chr10:43881372..43882946,2	MCF-7	breast:
9	chr10:43847403..43853479-chr10:43888233..43893881,11	MCF-7	breast:
10	chr10:43844606..43847679-chr10:43848074..43851632,6	MCF-7	breast:
11	chr10:43845683..43851518-chr10:43853877..43859694,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169813	Chromatin interaction
ENSG00000150201	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10409	0.86[ASN][1000 genomes]
rs10899790	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10899791	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899793	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899796	0.89[ASN][1000 genomes]
rs10899800	0.82[ASN][1000 genomes]
rs11238513	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11238514	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11238515	0.80[EUR][1000 genomes]
rs11238525	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238530	0.88[ASN][1000 genomes]
rs11238532	0.86[ASN][1000 genomes]
rs11238536	0.86[ASN][1000 genomes]
rs11814409	0.80[EUR][1000 genomes]
rs12220230	0.86[ASN][1000 genomes]
rs12220528	0.86[ASN][1000 genomes]
rs12250140	0.86[ASN][1000 genomes]
rs12261855	0.86[ASN][1000 genomes]
rs13376803	0.86[ASN][1000 genomes]
rs17153534	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879312	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4627023	0.90[EUR][1000 genomes]
rs4648316	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56198445	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57280597	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57479451	0.88[AFR][1000 genomes]
rs59383062	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7099802	0.86[ASN][1000 genomes]
rs7907179	0.86[ASN][1000 genomes]
rs7909500	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7921001	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][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

Variant related diseases (count:1)

Disease	PMID	Source
Telomere length	24478790	GWAS catalog

Chromatin state (count:46 , 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	chr10:43848400-43850800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr10:43848400-43851800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr10:43848600-43850000	Enhancers	Brain Angular Gyrus	brain
11	chr10:43848600-43850000	Enhancers	Brain Anterior Caudate	brain
12	chr10:43848600-43850000	Enhancers	Brain Cingulate Gyrus	brain
13	chr10:43848600-43850800	Enhancers	Brain Substantia Nigra	brain
14	chr10:43848600-43851400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr10:43848600-43851600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr10:43848600-43851800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr10:43848600-43852000	Enhancers	Brain Hippocampus Middle	brain
18	chr10:43848600-43852400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr10:43849000-43850800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr10:43849000-43851400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr10:43849000-43857000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr10:43849200-43850000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:43849200-43850000	Enhancers	Fetal Intestine Large	intestine
24	chr10:43849200-43850800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr10:43849200-43852000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr10:43849200-43852400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:43849200-43852600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:43849400-43850000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:43849400-43850400	Weak transcription	Stomach Mucosa	stomach
30	chr10:43849400-43850800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:43849400-43851200	Enhancers	Hela-S3	cervix
32	chr10:43849400-43852400	Enhancers	NHEK	skin
33	chr10:43849400-43852600	Enhancers	K562	blood
34	chr10:43849600-43850400	Weak transcription	HMEC	breast
35	chr10:43849600-43850800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr10:43849600-43851600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr10:43849800-43850000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:43849800-43850000	Enhancers	Duodenum Mucosa	Duodenum
39	chr10:43849800-43850000	Enhancers	Fetal Intestine Small	intestine
40	chr10:43849800-43850000	Enhancers	Pancreas	Pancrea
41	chr10:43849800-43850000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr10:43849800-43850000	Enhancers	HSMMtube	muscle
43	chr10:43849800-43850200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:43849800-43850600	Enhancers	Fetal Kidney	kidney
45	chr10:43849800-43850800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr10:43849800-43851200	Enhancers	A549	lung

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