Variant report

Variant	rs960946
Chromosome Location	chr15:57549054-57549055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57543547..57545308-chr15:57547959..57549638,2	K562	blood:
2	chr15:57539046..57541393-chr15:57548730..57551429,2	MCF-7	breast:
3	chr15:57548444..57552670-chr15:57553195..57556981,4	K562	blood:
4	chr15:57543333..57548085-chr15:57548138..57552930,5	K562	blood:
5	chr15:57548795..57550797-chr15:57550821..57552901,2	K562	blood:

Variant related genes	Relation type
ENSG00000260689	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1037956	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1037958	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10518899	0.81[EUR][1000 genomes]
rs11071309	0.83[ASN][1000 genomes]
rs11629653	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630910	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631084	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632069	0.85[ASN][1000 genomes]
rs11634352	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11635440	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636201	0.83[ASN][1000 genomes]
rs11636340	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636348	0.83[ASN][1000 genomes]
rs11636919	0.83[ASN][1000 genomes]
rs11637955	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11856073	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11857507	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11857722	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858783	0.85[ASN][1000 genomes]
rs12050751	0.80[EUR][1000 genomes]
rs12050758	0.80[EUR][1000 genomes]
rs12899036	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12899588	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12901671	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902099	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902170	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12902581	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903115	0.81[EUR][1000 genomes]
rs12903151	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903221	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904321	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904501	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904561	0.82[ASN][1000 genomes]
rs12904933	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12906042	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906335	0.86[ASN][1000 genomes]
rs12906566	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12908278	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908760	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12909016	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909696	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12910109	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12910832	0.83[ASN][1000 genomes]
rs12911256	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911297	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911518	0.82[EUR][1000 genomes]
rs12912210	0.83[ASN][1000 genomes]
rs12912353	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912868	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914425	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914481	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12915489	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916478	0.82[EUR][1000 genomes]
rs12917093	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1462156	0.82[EUR][1000 genomes]
rs1545728	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17239431	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17239508	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1814585	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1867641	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278685	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290938	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2414491	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2414492	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431023	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2441925	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593235	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2593237	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593238	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2733341	0.83[ASN][1000 genomes]
rs3794613	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4238321	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238322	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4303429	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4353440	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4369592	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4447362	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774251	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774252	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774913	0.83[ASN][1000 genomes]
rs4774918	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774919	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5014892	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61996955	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61996957	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62022237	0.81[ASN][1000 genomes]
rs7161965	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs745652	0.83[ASN][1000 genomes]
rs898901	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935326	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs978274	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
5	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
6	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
7	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
10	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:57528400-57554800	Weak transcription	NHEK	skin
12	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr15:57537000-57549200	Strong transcription	Dnd41	blood
16	chr15:57537800-57551600	Weak transcription	Brain Germinal Matrix	brain
17	chr15:57537800-57551800	Weak transcription	Small Intestine	intestine
18	chr15:57537800-57555200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
20	chr15:57538400-57551800	Weak transcription	Stomach Mucosa	stomach
21	chr15:57538400-57564800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:57538600-57551800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:57538800-57554200	Weak transcription	Fetal Brain Female	brain
24	chr15:57539400-57554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:57539600-57551400	Weak transcription	Brain Anterior Caudate	brain
27	chr15:57539600-57556800	Weak transcription	Gastric	stomach
28	chr15:57539600-57565200	Weak transcription	Aorta	Aorta
29	chr15:57539600-57565200	Weak transcription	Esophagus	oesophagus
30	chr15:57540000-57554400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:57540200-57551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr15:57540200-57555000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:57540600-57551800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:57540600-57556800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:57540600-57557000	Weak transcription	Lung	lung
36	chr15:57540600-57565400	Weak transcription	Ovary	ovary
37	chr15:57542200-57550400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:57542600-57550400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr15:57542600-57550600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr15:57543000-57556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:57543200-57549400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:57543200-57549800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:57543200-57550200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:57543200-57565200	Weak transcription	Right Ventricle	heart
45	chr15:57543400-57550600	Strong transcription	Primary T cells from cord blood	blood
46	chr15:57543800-57549200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:57544400-57550800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:57544400-57551600	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:57544400-57551600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:57544400-57551800	Weak transcription	Brain Angular Gyrus	brain

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