Variant report

Variant	rs16964507
Chromosome Location	chr15:52057004-52057005
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52026672..52029372-chr15:52056834..52058990,2	MCF-7	breast:
2	chr15:52035146..52037140-chr15:52056300..52058053,2	MCF-7	breast:
3	chr15:52054450..52058295-chr15:52061213..52063877,3	MCF-7	breast:
4	chr15:52047517..52051526-chr15:52055116..52057120,3	K562	blood:
5	chr15:52044048..52045789-chr15:52054903..52057784,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259377	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs16953082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[EUR][1000 genomes]
rs16964486	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16964488	1.00[CEU][hapmap]
rs16964505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16964506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964510	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964518	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964528	0.88[EUR][1000 genomes]
rs16964532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];0.95[EUR][1000 genomes]
rs16964555	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16964561	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];0.90[EUR][1000 genomes]
rs16964579	0.90[EUR][1000 genomes]
rs16964585	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16964596	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];0.90[EUR][1000 genomes]
rs16964639	0.83[EUR][1000 genomes]
rs16964645	0.85[EUR][1000 genomes]
rs17705373	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2414115	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2570232	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs2623256	0.84[EUR][1000 genomes]
rs2899478	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3751595	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs3794529	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4775971	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs56221158	0.97[EUR][1000 genomes]
rs7165594	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7166954	0.86[EUR][1000 genomes]
rs7167759	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7174616	1.00[CEU][hapmap]
rs7175121	1.00[CEU][hapmap]
rs7179971	0.86[EUR][1000 genomes]
rs7180093	0.86[EUR][1000 genomes]
rs73405364	0.80[EUR][1000 genomes]
rs7342575	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs74015757	0.91[EUR][1000 genomes]
rs74015761	0.91[EUR][1000 genomes]
rs8036648	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52044600-52060000	Weak transcription	Esophagus	oesophagus
2	chr15:52044600-52060200	Weak transcription	Aorta	Aorta
3	chr15:52044800-52060000	Weak transcription	Spleen	Spleen
4	chr15:52045000-52060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:52046800-52060000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr15:52048000-52058000	Weak transcription	Primary T cells from cord blood	blood
7	chr15:52048200-52060000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:52048200-52060200	Weak transcription	Thymus	Thymus
9	chr15:52049200-52060000	Weak transcription	Dnd41	blood
10	chr15:52049400-52059800	Weak transcription	Primary B cells from cord blood	blood
11	chr15:52049800-52059800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:52051200-52060000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:52051200-52060000	Weak transcription	Lung	lung
14	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
15	chr15:52051400-52060000	Weak transcription	Fetal Brain Female	brain
16	chr15:52051400-52060200	Weak transcription	Adipose Nuclei	Adipose
17	chr15:52051400-52060400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:52051400-52061200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
21	chr15:52052200-52060000	Weak transcription	Left Ventricle	heart
22	chr15:52052200-52060000	Weak transcription	Ovary	ovary
23	chr15:52052200-52060200	Weak transcription	Right Ventricle	heart
24	chr15:52052200-52060800	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:52052200-52061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:52052200-52064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
28	chr15:52052200-52068600	Weak transcription	HMEC	breast
29	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
31	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
32	chr15:52052400-52060000	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:52052400-52060200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:52052400-52060200	Weak transcription	Fetal Lung	lung
35	chr15:52052400-52060600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:52052400-52061000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:52052400-52067000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
39	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
40	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr15:52052600-52060000	Weak transcription	NHLF	lung
42	chr15:52052600-52060400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr15:52052600-52065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:52052600-52106600	Weak transcription	HSMM	muscle
45	chr15:52053000-52060000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:52053400-52058200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr15:52053400-52058200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:52053400-52060000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
50	chr15:52053600-52060200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links