Variant report

Variant	rs10520145
Chromosome Location	chr15:39958679-39958680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39159362..39162294-chr15:39956863..39959269,2	MCF-7	breast:
2	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
3	chr15:39947922..39949877-chr15:39956880..39959494,2	MCF-7	breast:
4	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
5	chr15:39892943..39897047-chr15:39958260..39961815,3	MCF-7	breast:
6	chr15:39930109..39933577-chr15:39957965..39961029,3	MCF-7	breast:
7	chr15:39880858..39882664-chr15:39957984..39960909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10520141	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10520143	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10520146	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10520148	1.00[ASN][1000 genomes]
rs10520149	0.83[EUR][1000 genomes]
rs10520150	0.83[EUR][1000 genomes]
rs10520152	1.00[JPT][hapmap]
rs1073675	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12324669	0.83[EUR][1000 genomes]
rs12324682	1.00[JPT][hapmap]
rs16969335	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969484	0.86[ASN][1000 genomes]
rs16969487	1.00[JPT][hapmap]
rs16969491	1.00[CHB][hapmap]
rs16969547	0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16969573	0.86[ASN][1000 genomes]
rs16969662	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969663	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969664	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969666	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969678	0.86[ASN][1000 genomes]
rs16969679	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969680	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969688	0.88[GIH][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16969692	0.88[GIH][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16969701	0.83[EUR][1000 genomes]
rs16969702	0.83[EUR][1000 genomes]
rs16969718	0.83[EUR][1000 genomes]
rs16969723	0.83[EUR][1000 genomes]
rs16969724	0.83[EUR][1000 genomes]
rs17706083	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1994380	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2129455	0.83[EUR][1000 genomes]
rs2129457	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2171309	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs2228262	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2411316	1.00[JPT][hapmap]
rs2618165	1.00[JPT][hapmap]
rs28417668	0.83[EUR][1000 genomes]
rs28421798	0.82[EUR][1000 genomes]
rs28457210	0.83[EUR][1000 genomes]
rs28514641	0.83[EUR][1000 genomes]
rs28519658	0.83[EUR][1000 genomes]
rs28568868	0.83[EUR][1000 genomes]
rs28570392	0.83[EUR][1000 genomes]
rs28585060	0.83[EUR][1000 genomes]
rs28625134	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28626090	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28629181	0.83[EUR][1000 genomes]
rs28657849	0.83[EUR][1000 genomes]
rs28691633	0.83[EUR][1000 genomes]
rs28735552	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28785006	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34878675	1.00[ASN][1000 genomes]
rs4085744	1.00[ASN][1000 genomes]
rs4322636	0.86[ASN][1000 genomes]
rs4415979	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4503768	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55674415	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55899942	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56862147	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56916119	0.83[EUR][1000 genomes]
rs58878379	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59146042	0.86[ASN][1000 genomes]
rs60228643	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60613947	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7171057	0.83[EUR][1000 genomes]
rs7172138	0.83[EUR][1000 genomes]
rs7172155	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7172346	0.83[EUR][1000 genomes]
rs7173948	0.86[GIH][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7180740	0.83[EUR][1000 genomes]
rs7181354	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7181875	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7182423	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7183462	0.88[GIH][hapmap];0.83[EUR][1000 genomes]
rs72727029	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727047	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72727060	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72727067	0.83[EUR][1000 genomes]
rs72727068	0.83[EUR][1000 genomes]
rs72727070	0.83[EUR][1000 genomes]
rs74008680	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74008683	0.83[EUR][1000 genomes]
rs8036035	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8041266	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs880270	1.00[JPT][hapmap]
rs937961	0.88[GIH][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs937962	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9972350	1.00[CHD][hapmap];1.00[JPT][hapmap]

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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39954400-39959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:39955600-39959800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:39955800-39960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:39955800-39960200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr15:39956000-39958800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr15:39956000-39958800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr15:39956000-39960200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:39956400-39959000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:39956400-39959000	Weak transcription	NHLF	lung
10	chr15:39956600-39959200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:39956600-39959800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr15:39956600-39960000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr15:39956800-39959200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:39956800-39959800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr15:39956800-39961400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:39957000-39958800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:39957000-39959000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:39957000-39959200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:39957200-39961000	Enhancers	HSMMtube	muscle
20	chr15:39957400-39959000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:39957600-39961200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:39957800-39959400	Enhancers	HUVEC	blood vessel
23	chr15:39958000-39959600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr15:39958000-39960200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:39958200-39959200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:39958200-39959400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr15:39958200-39959400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:39958200-39959400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:39958200-39959400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:39958200-39959600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr15:39958200-39959800	Enhancers	Fetal Lung	lung
32	chr15:39958200-39959800	Enhancers	NH-A	brain
33	chr15:39958200-39960200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:39958200-39961000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:39958400-39959200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr15:39958400-39959400	Enhancers	Osteobl	bone
37	chr15:39958400-39959800	Enhancers	Aorta	Aorta
38	chr15:39958400-39960000	Enhancers	Fetal Kidney	kidney
39	chr15:39958400-39960200	Enhancers	HSMM	muscle
40	chr15:39958600-39959800	Weak transcription	Liver	Liver
41	chr15:39958600-39960200	Enhancers	Colon Smooth Muscle	Colon

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