Variant report

Variant	rs2959933
Chromosome Location	chr15:72594712-72594713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72594284..72596932-chr15:72765825..72768164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261423	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10220850	1.00[CEU][hapmap]
rs10518987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11632505	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12324744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12899442	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12904378	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12904667	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906356	0.94[ASN][1000 genomes]
rs12906612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12906942	1.00[CEU][hapmap]
rs12907087	0.94[ASN][1000 genomes]
rs12907377	0.94[ASN][1000 genomes]
rs12907707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908863	0.88[ASN][1000 genomes]
rs12908883	1.00[CEU][hapmap]
rs12909590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12910475	0.88[ASN][1000 genomes]
rs12911285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12914269	0.94[ASN][1000 genomes]
rs12914312	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12916039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12916226	0.94[ASN][1000 genomes]
rs12916298	0.88[ASN][1000 genomes]
rs12917402	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1426169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2288257	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28573838	0.82[EUR][1000 genomes]
rs2912203	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912204	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912211	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs2912212	0.83[YRI][hapmap]
rs2912215	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912218	0.82[ASW][hapmap];0.80[YRI][hapmap]
rs2912221	1.00[CEU][hapmap]
rs2912222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912223	1.00[CEU][hapmap]
rs2912224	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957751	0.82[ASN][1000 genomes]
rs2957752	0.88[ASN][1000 genomes]
rs2959905	0.84[AFR][1000 genomes]
rs2959916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959917	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959920	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2959923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959924	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959925	1.00[CEU][hapmap]
rs2959926	1.00[CEU][hapmap]
rs2959927	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959928	0.86[AFR][1000 genomes]
rs2959929	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959931	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959934	0.88[AFR][1000 genomes]
rs2959935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959940	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34023258	0.88[ASN][1000 genomes]
rs34115124	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34211376	1.00[ASN][1000 genomes]
rs34294127	0.88[ASN][1000 genomes]
rs34346715	0.94[ASN][1000 genomes]
rs34362323	0.88[ASN][1000 genomes]
rs34382909	0.94[ASN][1000 genomes]
rs34505994	0.88[ASN][1000 genomes]
rs34511502	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34538801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34658339	0.94[ASN][1000 genomes]
rs34677662	1.00[ASN][1000 genomes]
rs34694253	0.88[ASN][1000 genomes]
rs34705283	0.88[ASN][1000 genomes]
rs34789424	0.88[ASN][1000 genomes]
rs34815962	0.94[ASN][1000 genomes]
rs35071085	0.88[ASN][1000 genomes]
rs35104697	0.94[ASN][1000 genomes]
rs35144689	0.88[ASN][1000 genomes]
rs35202897	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35259670	0.88[ASN][1000 genomes]
rs35285520	0.94[ASN][1000 genomes]
rs35362359	0.88[ASN][1000 genomes]
rs35378070	0.94[ASN][1000 genomes]
rs35457238	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35514603	0.82[AFR][1000 genomes]
rs35554838	0.88[ASN][1000 genomes]
rs35694406	0.94[ASN][1000 genomes]
rs36110969	0.94[ASN][1000 genomes]
rs3743227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3743228	0.94[ASN][1000 genomes]
rs3743229	0.94[ASN][1000 genomes]
rs3759901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3825949	0.83[ASN][1000 genomes]
rs4776592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4776593	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4777501	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs57420281	0.94[ASN][1000 genomes]
rs57692836	0.94[ASN][1000 genomes]
rs58352854	0.94[ASN][1000 genomes]
rs66608810	0.94[ASN][1000 genomes]
rs67195650	0.94[ASN][1000 genomes]
rs71395058	0.88[ASN][1000 genomes]
rs71395061	0.88[ASN][1000 genomes]
rs71395066	0.94[ASN][1000 genomes]
rs71395068	0.94[ASN][1000 genomes]
rs71395070	0.94[ASN][1000 genomes]
rs71395074	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71397231	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71397232	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71397233	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71411063	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169150	0.94[ASN][1000 genomes]
rs7174264	0.83[ASN][1000 genomes]
rs73438446	0.94[ASN][1000 genomes]
rs8192359	0.94[ASN][1000 genomes]
rs8192387	0.94[ASN][1000 genomes]
rs8192397	0.94[ASN][1000 genomes]
rs9672916	1.00[CEU][hapmap]
rs9806184	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs9806204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72566000-72611400	Weak transcription	Right Ventricle	heart
2	chr15:72567000-72611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:72573200-72603000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:72573800-72595000	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:72573800-72595000	Weak transcription	Brain Substantia Nigra	brain
6	chr15:72573800-72596200	Weak transcription	Liver	Liver
7	chr15:72573800-72597200	Weak transcription	Brain Anterior Caudate	brain
8	chr15:72574400-72595000	Weak transcription	Lung	lung
9	chr15:72578000-72611800	Weak transcription	Ovary	ovary
10	chr15:72579000-72598200	Weak transcription	Brain Germinal Matrix	brain
11	chr15:72579600-72602400	Weak transcription	Primary T cells from cord blood	blood
12	chr15:72580800-72595000	Weak transcription	Adipose Nuclei	Adipose
13	chr15:72580800-72598200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:72581000-72595200	Weak transcription	Brain Angular Gyrus	brain
15	chr15:72581200-72598600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:72581600-72594800	Weak transcription	Fetal Intestine Small	intestine
17	chr15:72582000-72608000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:72582000-72611800	Weak transcription	Spleen	Spleen
19	chr15:72582600-72595000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:72582600-72598600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:72583800-72611600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:72585600-72598200	Weak transcription	Fetal Stomach	stomach
23	chr15:72590200-72604800	Weak transcription	Aorta	Aorta
24	chr15:72590600-72607600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:72590800-72602000	Weak transcription	Left Ventricle	heart
26	chr15:72592600-72597600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:72594400-72596800	Weak transcription	Primary B cells from cord blood	blood

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