Variant report

Variant	rs10520146
Chromosome Location	chr15:39959465-39959466
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:39920700..39923129-chr15:39958970..39962199,4	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	chr15:39890163..39892186-chr15:39958834..39961393,2	MCF-7	breast:
6	chr15:39892943..39897047-chr15:39958260..39961815,3	MCF-7	breast:
7	chr15:39930109..39933577-chr15:39957965..39961029,3	MCF-7	breast:
8	chr15:39878927..39880641-chr15:39959246..39961103,2	MCF-7	breast:
9	chr15:39880858..39882664-chr15:39957984..39960909,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10152903	1.00[CHB][hapmap]
rs10152951	1.00[CHB][hapmap]
rs1051442	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10520141	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10520143	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10520145	1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520152	1.00[JPT][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12324682	1.00[JPT][hapmap]
rs1382443	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1382444	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs16969167	1.00[CHB][hapmap]
rs16969335	1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969484	0.86[ASN][1000 genomes]
rs16969487	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969491	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16969547	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969573	0.86[ASN][1000 genomes]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969678	0.86[ASN][1000 genomes]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17632916	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs17633107	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs17633210	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17705806	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17706083	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17706179	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17717859	1.00[CHB][hapmap]
rs1994380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228262	1.00[CHB][hapmap]
rs2228263	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2411316	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2618161	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2618164	0.91[CEU][hapmap]
rs2618165	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2618167	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs2664138	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs28377784	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28549326	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28619289	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28653011	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28735552	1.00[ASN][1000 genomes]
rs28785006	1.00[ASN][1000 genomes]
rs34878675	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4085744	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41315060	0.81[EUR][1000 genomes]
rs4322636	0.86[ASN][1000 genomes]
rs4415979	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4503768	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45461294	0.83[EUR][1000 genomes]
rs4923835	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs58188999	0.84[EUR][1000 genomes]
rs59146042	0.86[ASN][1000 genomes]
rs59578395	0.84[EUR][1000 genomes]
rs59628570	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60228643	1.00[ASN][1000 genomes]
rs6492905	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7179604	1.00[CHB][hapmap]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs72727029	1.00[ASN][1000 genomes]
rs74008647	0.84[EUR][1000 genomes]
rs74008648	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8036035	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8041266	1.00[CHB][hapmap]
rs880270	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs954152	0.80[EUR][1000 genomes]
rs9972350	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[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	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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39955600-39959800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:39955800-39960200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:39955800-39960200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr15:39956000-39960200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:39956600-39959800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr15:39956600-39960000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr15:39956800-39959800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr15:39956800-39961400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:39957200-39961000	Enhancers	HSMMtube	muscle
10	chr15:39957600-39961200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:39958000-39959600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:39958000-39960200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:39958200-39959600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr15:39958200-39959800	Enhancers	Fetal Lung	lung
15	chr15:39958200-39959800	Enhancers	NH-A	brain
16	chr15:39958200-39960200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:39958200-39961000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:39958400-39959800	Enhancers	Aorta	Aorta
19	chr15:39958400-39960000	Enhancers	Fetal Kidney	kidney
20	chr15:39958400-39960200	Enhancers	HSMM	muscle
21	chr15:39958600-39959800	Weak transcription	Liver	Liver
22	chr15:39958600-39960200	Enhancers	Colon Smooth Muscle	Colon
23	chr15:39958800-39960000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:39958800-39960000	Enhancers	Fetal Stomach	stomach
25	chr15:39958800-39960000	Enhancers	Stomach Smooth Muscle	stomach
26	chr15:39958800-39960200	Enhancers	NHDF-Ad	bronchial
27	chr15:39959000-39959800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:39959000-39959800	Enhancers	NHLF	lung
29	chr15:39959000-39960000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr15:39959000-39960200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr15:39959200-39959800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:39959200-39959800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr15:39959200-39960000	Enhancers	Right Atrium	heart
34	chr15:39959200-39960200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr15:39959200-39960200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:39959200-39960400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr15:39959200-39960800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:39959200-39961200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:39959400-39960800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:39959400-39962800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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