Variant report

Variant	rs6492911
Chromosome Location	chr15:39961452-39961453
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: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	chr15:39922048..39922709-chr15:39960306..39961692,3	MCF-7	breast:
2	chr15:39959771..39962008-chr15:40012951..40014930,2	MCF-7	breast:
3	chr15:39920700..39923129-chr15:39958970..39962199,4	MCF-7	breast:
4	chr15:39870612..39877795-chr15:39952369..39962860,18	MCF-7	breast:
5	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
6	chr15:39926188..39928117-chr15:39960668..39962621,2	MCF-7	breast:
7	chr15:39892943..39897047-chr15:39958260..39961815,3	MCF-7	breast:
8	chr15:39960300..39964337-chr15:39967513..39971099,4	K562	blood:
9	chr15:39961034..39963192-chr15:39965564..39967491,2	MCF-7	breast:
10	chr15:39960868..39962395-chr15:39964357..39966165,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10520142	0.83[YRI][hapmap]
rs1105159	0.91[CHB][hapmap]
rs11070231	0.87[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11631820	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs11631824	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12050804	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12899323	0.92[ASN][1000 genomes]
rs12900024	0.88[ASN][1000 genomes]
rs12900583	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12901142	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs12903514	0.94[ASN][1000 genomes]
rs12911549	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs12911999	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1906152	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1906155	0.87[ASN][1000 genomes]
rs1906156	0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1994379	0.86[CHB][hapmap]
rs2129459	0.87[ASN][1000 genomes]
rs2411299	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2411300	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2411301	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2411304	0.82[ASN][1000 genomes]
rs2411307	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2411308	0.92[ASN][1000 genomes]
rs2411309	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs2411310	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2411311	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2631697	0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631700	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631701	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2631702	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631704	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2631705	0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2631710	0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2664125	0.91[ASN][1000 genomes]
rs2664133	0.86[ASN][1000 genomes]
rs2664135	0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28437905	0.94[ASN][1000 genomes]
rs28581473	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898685	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs3103065	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs4319738	0.99[ASN][1000 genomes]
rs4429263	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4476148	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4480779	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4493017	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs4505280	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs4572354	0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4591113	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4606692	0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4924376	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924377	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6492909	0.95[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs6492910	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs68183224	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7167100	0.94[ASN][1000 genomes]
rs7170335	0.81[YRI][hapmap]
rs7177857	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7179013	0.95[CHB][hapmap]
rs8033902	0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs8034543	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8034885	0.93[ASN][1000 genomes]
rs8035354	0.98[ASN][1000 genomes]
rs8036226	0.94[ASN][1000 genomes]
rs8042068	0.93[ASN][1000 genomes]
rs937960	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs951358	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs9672572	0.87[ASN][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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39959400-39962800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:39959800-39961600	Weak transcription	Aorta	Aorta
3	chr15:39960200-39962400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:39960200-39964400	Weak transcription	HSMM	muscle
5	chr15:39960200-39972600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:39960800-39961600	Enhancers	Left Ventricle	heart
7	chr15:39960800-39961600	Enhancers	Ovary	ovary
8	chr15:39960800-39961600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr15:39960800-39962200	Enhancers	Rectal Smooth Muscle	rectum
10	chr15:39960800-39963000	Enhancers	Fetal Lung	lung
11	chr15:39961000-39964200	Weak transcription	HSMMtube	muscle
12	chr15:39961200-39961600	Enhancers	Lung	lung
13	chr15:39961200-39961600	Enhancers	Pancreas	Pancrea
14	chr15:39961200-39961600	Enhancers	Psoas Muscle	Psoas
15	chr15:39961200-39961600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr15:39961200-39961600	Enhancers	Spleen	Spleen
17	chr15:39961200-39961800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:39961400-39961600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:39961400-39961600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:39961400-39961600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:39961400-39961600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:39961400-39962000	Enhancers	Fetal Kidney	kidney

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