Variant report

Variant	rs17649047
Chromosome Location	chr15:52053229-52053230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52028181..52032954-chr15:52050508..52053619,6	MCF-7	breast:
2	chr15:52048901..52051193-chr15:52052461..52055031,2	MCF-7	breast:
3	chr15:52043943..52045698-chr15:52052374..52055124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction
ENSG00000259377	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1025185	1.00[EUR][1000 genomes]
rs10519323	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519325	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs10519326	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs12438469	1.00[EUR][1000 genomes]
rs12442283	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1378891	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1426085	1.00[EUR][1000 genomes]
rs1426086	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs16964523	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs17649178	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17649208	1.00[JPT][hapmap]
rs17649255	0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649391	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs17649692	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs17649801	1.00[EUR][1000 genomes]
rs17705530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17705649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17705685	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17705889	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs17706076	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2052707	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2162224	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs2414118	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2436664	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2470613	1.00[EUR][1000 genomes]
rs2554309	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2554310	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2554311	1.00[EUR][1000 genomes]
rs2554318	1.00[EUR][1000 genomes]
rs2554321	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2554323	1.00[EUR][1000 genomes]
rs2554325	1.00[EUR][1000 genomes]
rs2554326	1.00[EUR][1000 genomes]
rs2554330	1.00[EUR][1000 genomes]
rs2554333	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2554341	0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2554351	1.00[EUR][1000 genomes]
rs2554352	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2554356	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570218	0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2570219	1.00[EUR][1000 genomes]
rs2570220	1.00[EUR][1000 genomes]
rs2570221	1.00[EUR][1000 genomes]
rs2570227	1.00[EUR][1000 genomes]
rs2570232	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2570242	0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2570244	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570245	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570247	1.00[EUR][1000 genomes]
rs2570249	0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2570250	0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2570256	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570257	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570259	1.00[EUR][1000 genomes]
rs2570261	1.00[EUR][1000 genomes]
rs2570267	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570270	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2570273	0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2570274	1.00[EUR][1000 genomes]
rs2593165	1.00[EUR][1000 genomes]
rs2593175	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2593176	1.00[EUR][1000 genomes]
rs2593180	1.00[EUR][1000 genomes]
rs2623246	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2623248	0.86[JPT][hapmap]
rs2623250	0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2623252	1.00[EUR][1000 genomes]
rs2623257	1.00[EUR][1000 genomes]
rs2623260	1.00[EUR][1000 genomes]
rs2623264	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2623267	1.00[EUR][1000 genomes]
rs2623268	1.00[EUR][1000 genomes]
rs2623269	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2623277	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2623278	1.00[EUR][1000 genomes]
rs2623287	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs2899483	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2916174	1.00[EUR][1000 genomes]
rs2959297	1.00[EUR][1000 genomes]
rs2959303	1.00[EUR][1000 genomes]
rs3099570	1.00[EUR][1000 genomes]
rs34407523	1.00[EUR][1000 genomes]
rs36097346	0.89[ASN][1000 genomes]
rs3794533	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774600	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775971	0.81[CHD][hapmap];0.97[AMR][1000 genomes]
rs4775979	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4775987	1.00[EUR][1000 genomes]
rs4775988	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs4775989	1.00[EUR][1000 genomes]
rs56221158	0.84[AMR][1000 genomes]
rs7166322	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7166954	0.89[AMR][1000 genomes]
rs7170429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7170700	1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7179139	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7179971	0.84[AMR][1000 genomes]
rs7180093	0.84[AMR][1000 genomes]
rs72730966	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73407386	0.89[ASN][1000 genomes]
rs73407396	0.89[ASN][1000 genomes]
rs73411105	1.00[EUR][1000 genomes]
rs74015757	0.84[AMR][1000 genomes]
rs74015761	0.82[AMR][1000 genomes]
rs8024441	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026507	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027426	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8042310	1.00[EUR][1000 genomes]
rs919056	0.86[JPT][hapmap]
rs919057	0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs990666	0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[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:61 , 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	chr15:52045200-52053400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:52046800-52060000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:52047200-52053600	Enhancers	Brain Cingulate Gyrus	brain
8	chr15:52047400-52053600	Enhancers	Brain Hippocampus Middle	brain
9	chr15:52048000-52058000	Weak transcription	Primary T cells from cord blood	blood
10	chr15:52048200-52060000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:52048200-52060200	Weak transcription	Thymus	Thymus
12	chr15:52049200-52053400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr15:52049200-52060000	Weak transcription	Dnd41	blood
14	chr15:52049400-52059800	Weak transcription	Primary B cells from cord blood	blood
15	chr15:52049800-52053400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:52049800-52059800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:52051200-52060000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:52051200-52060000	Weak transcription	Lung	lung
19	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
20	chr15:52051400-52053400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr15:52051400-52053600	Enhancers	Brain Substantia Nigra	brain
22	chr15:52051400-52060000	Weak transcription	Fetal Brain Female	brain
23	chr15:52051400-52060200	Weak transcription	Adipose Nuclei	Adipose
24	chr15:52051400-52060400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:52051400-52061200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
28	chr15:52052200-52056800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:52052200-52060000	Weak transcription	Left Ventricle	heart
30	chr15:52052200-52060000	Weak transcription	Ovary	ovary
31	chr15:52052200-52060200	Weak transcription	Right Ventricle	heart
32	chr15:52052200-52060800	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:52052200-52061200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:52052200-52064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
36	chr15:52052200-52068600	Weak transcription	HMEC	breast
37	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
39	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
40	chr15:52052400-52053600	Weak transcription	Right Atrium	heart
41	chr15:52052400-52060000	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:52052400-52060200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:52052400-52060200	Weak transcription	Fetal Lung	lung
44	chr15:52052400-52060600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:52052400-52061000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:52052400-52067000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
48	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
49	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:52052600-52056600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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