Variant report

Variant	rs2959297
Chromosome Location	chr15:52261552-52261553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52261233..52265470-chr15:52469433..52474401,7	MCF-7	breast:
2	chr15:52257155..52261897-chr15:52262401..52265766,14	MCF-7	breast:
3	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000166477	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1025185	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519323	1.00[EUR][1000 genomes]
rs10519325	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10519326	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12438469	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1426085	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1426086	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17649047	1.00[EUR][1000 genomes]
rs17649178	1.00[EUR][1000 genomes]
rs17649255	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17649391	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17649692	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17649801	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17649820	0.84[AMR][1000 genomes]
rs17649826	0.84[AMR][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17706076	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1867985	0.83[AFR][1000 genomes]
rs2052707	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2162224	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250797	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs2263946	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2433219	0.81[AMR][1000 genomes]
rs2436664	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470606	0.86[AFR][1000 genomes]
rs2470609	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2470613	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2554309	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554310	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554311	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554317	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2554318	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2554321	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2554323	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554325	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2554326	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2554330	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2554333	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554338	0.90[AMR][1000 genomes]
rs2554341	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2554346	0.83[AFR][1000 genomes]
rs2554351	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554352	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554356	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2570218	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570219	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570220	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570221	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570225	0.87[ASN][1000 genomes]
rs2570227	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570234	0.85[ASN][1000 genomes]
rs2570242	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570244	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2570245	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570246	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2570247	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2570249	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2570250	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2570256	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570257	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570259	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570261	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2570262	0.83[AMR][1000 genomes]
rs2570267	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570270	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2570272	0.83[AFR][1000 genomes]
rs2570273	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570274	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593165	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593175	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593176	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593180	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593186	0.83[AFR][1000 genomes]
rs2593196	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs2593203	0.86[AFR][1000 genomes]
rs2623246	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2623248	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2623250	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623252	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623253	0.85[ASN][1000 genomes]
rs2623257	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2623260	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623264	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623267	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2623268	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623269	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2623277	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623278	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623287	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623293	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes]
rs2916174	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959303	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3099570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34407523	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35487339	0.92[AMR][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4775988	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775989	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59782457	0.81[AMR][1000 genomes]
rs7166322	1.00[EUR][1000 genomes]
rs7170429	1.00[EUR][1000 genomes]
rs7170700	1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73396698	0.89[AFR][1000 genomes]
rs73411105	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74013606	0.85[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	1.00[EUR][1000 genomes]
rs8042310	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919056	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs919057	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs990666	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv569410	chr15:52257874-52273132	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
2	chr15:52244600-52262600	Weak transcription	Fetal Heart	heart
3	chr15:52245600-52261800	Weak transcription	Pancreas	Pancrea
4	chr15:52245600-52262600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:52245800-52263000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:52245800-52263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52246400-52262200	Weak transcription	NHLF	lung
8	chr15:52247000-52262400	Weak transcription	Colonic Mucosa	Colon
9	chr15:52249800-52263000	Weak transcription	Psoas Muscle	Psoas
10	chr15:52253200-52262400	Weak transcription	Fetal Brain Male	brain
11	chr15:52253200-52262800	Weak transcription	HSMMtube	muscle
12	chr15:52253200-52263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:52253400-52262400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:52253400-52262400	Weak transcription	Esophagus	oesophagus
15	chr15:52253600-52263000	Weak transcription	Right Ventricle	heart
16	chr15:52253800-52261800	Weak transcription	Small Intestine	intestine
17	chr15:52253800-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:52253800-52263200	Weak transcription	Gastric	stomach
19	chr15:52254200-52261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:52254200-52262200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:52254200-52262400	Weak transcription	Spleen	Spleen
22	chr15:52254200-52262600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:52254200-52262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:52254200-52263200	Weak transcription	Left Ventricle	heart
25	chr15:52254400-52261800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:52254400-52262400	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:52254400-52263000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:52254400-52263200	Weak transcription	Ovary	ovary
29	chr15:52254600-52261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:52254600-52262800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:52255000-52262000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:52255000-52262000	Weak transcription	K562	blood
33	chr15:52255000-52262200	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:52255000-52262200	Weak transcription	HMEC	breast
35	chr15:52255000-52262400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:52255000-52262400	Weak transcription	HSMM	muscle
37	chr15:52255200-52262000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:52255600-52262400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:52257800-52263000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr15:52258000-52262000	Weak transcription	NHDF-Ad	bronchial
41	chr15:52258000-52262200	Weak transcription	Osteobl	bone
42	chr15:52258200-52262600	Weak transcription	NH-A	brain
43	chr15:52258400-52261800	Weak transcription	Liver	Liver
44	chr15:52258400-52262200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:52258400-52262200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:52258400-52262200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:52258400-52262600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:52258600-52261600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:52258600-52261800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:52258600-52262000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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