Variant report

Variant	rs12440617
Chromosome Location	chr15:93257002-93257003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93250790..93254703-chr15:93255991..93258300,4	MCF-7	breast:
2	chr15:93195935..93200377-chr15:93256556..93260471,5	MCF-7	breast:
3	chr15:93155538..93157198-chr15:93256729..93258273,2	MCF-7	breast:
4	chr15:93187273..93189424-chr15:93256884..93259260,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1004309	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11854403	0.88[EUR][1000 genomes]
rs11854426	0.88[EUR][1000 genomes]
rs12439654	0.96[ASN][1000 genomes]
rs12440201	0.96[ASN][1000 genomes]
rs12442362	0.96[ASN][1000 genomes]
rs12442555	0.96[ASN][1000 genomes]
rs12899027	0.88[EUR][1000 genomes]
rs12906973	0.90[ASN][1000 genomes]
rs1545143	0.88[EUR][1000 genomes]
rs1561304	0.87[ASN][1000 genomes]
rs17648050	0.85[ASN][1000 genomes]
rs1808818	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1971808	0.84[EUR][1000 genomes]
rs2018744	0.85[EUR][1000 genomes]
rs2278519	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2278520	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2387911	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2387913	0.84[EUR][1000 genomes]
rs2387914	0.83[EUR][1000 genomes]
rs2387915	0.90[EUR][1000 genomes]
rs34888918	0.87[EUR][1000 genomes]
rs34981968	0.88[EUR][1000 genomes]
rs35095971	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35244027	0.88[EUR][1000 genomes]
rs35663415	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35770033	0.88[EUR][1000 genomes]
rs35982819	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4777731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4777734	0.90[EUR][1000 genomes]
rs4778033	0.91[ASN][1000 genomes]
rs4778034	0.88[EUR][1000 genomes]
rs57030748	0.85[EUR][1000 genomes]
rs58407306	0.87[EUR][1000 genomes]
rs58894958	0.90[ASN][1000 genomes]
rs60471977	0.90[EUR][1000 genomes]
rs6496972	0.87[EUR][1000 genomes]
rs6496973	0.90[EUR][1000 genomes]
rs6496974	0.90[EUR][1000 genomes]
rs6496975	0.90[EUR][1000 genomes]
rs6496976	0.90[EUR][1000 genomes]
rs6496977	0.88[EUR][1000 genomes]
rs6496978	0.89[EUR][1000 genomes]
rs6496979	0.88[EUR][1000 genomes]
rs6496982	0.88[EUR][1000 genomes]
rs6496985	0.86[EUR][1000 genomes]
rs66824972	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66899661	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67770259	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67971141	0.88[EUR][1000 genomes]
rs71462507	0.88[EUR][1000 genomes]
rs7165223	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7166307	0.88[EUR][1000 genomes]
rs7169452	0.88[EUR][1000 genomes]
rs7170733	0.90[EUR][1000 genomes]
rs7174515	0.88[EUR][1000 genomes]
rs7176732	0.87[EUR][1000 genomes]
rs7176911	0.87[EUR][1000 genomes]
rs7176935	0.88[EUR][1000 genomes]
rs7177028	0.88[EUR][1000 genomes]
rs7183236	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025793	0.89[EUR][1000 genomes]
rs8028966	0.88[EUR][1000 genomes]
rs8029984	0.90[EUR][1000 genomes]
rs8032004	0.90[EUR][1000 genomes]
rs8033632	0.88[EUR][1000 genomes]
rs8033698	0.85[EUR][1000 genomes]
rs8039425	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8039858	0.90[EUR][1000 genomes]
rs8041556	0.88[EUR][1000 genomes]
rs8042909	0.88[EUR][1000 genomes]
rs9806135	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv974620	chr15:93252874-93258773	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93245600-93257400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:93246200-93257400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:93249400-93257400	Weak transcription	Brain Substantia Nigra	brain
4	chr15:93249600-93257200	Weak transcription	Brain Anterior Caudate	brain
5	chr15:93250200-93257200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:93253200-93257200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:93253200-93257200	Weak transcription	HUVEC	blood vessel
8	chr15:93253400-93257200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:93254800-93257400	Weak transcription	Lung	lung
10	chr15:93255200-93257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:93255800-93257200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:93256600-93258400	Active TSS	Ovary	ovary
13	chr15:93256800-93257200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr15:93256800-93257200	Enhancers	Rectal Smooth Muscle	rectum
15	chr15:93256800-93257400	Enhancers	Colon Smooth Muscle	Colon
16	chr15:93257000-93257200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:93257000-93257200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr15:93257000-93257200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:93257000-93257200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:93257000-93257200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:93257000-93257200	Enhancers	Brain Germinal Matrix	brain
22	chr15:93257000-93257200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:93257000-93257200	Enhancers	Fetal Brain Male	brain
24	chr15:93257000-93257200	Enhancers	Fetal Kidney	kidney
25	chr15:93257000-93257200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr15:93257000-93257200	Enhancers	Stomach Smooth Muscle	stomach
27	chr15:93257000-93257200	Enhancers	NH-A	brain
28	chr15:93257000-93257200	Enhancers	Osteobl	bone
29	chr15:93257000-93257400	Enhancers	Fetal Muscle Leg	muscle
30	chr15:93257000-93257600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:93257000-93258200	Active TSS	Fetal Lung	lung

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