Variant report

Variant	rs1956893
Chromosome Location	chr14:24929392-24929393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:24910451..24913467-chr14:24926014..24930297,6	MCF-7	breast:
2	chr14:24929358..24930887-chr8:102503029..102505102,2	MCF-7	breast:
3	chr14:24923545..24925251-chr14:24928583..24930504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254024	Chromatin interaction
ENSG00000083307	Chromatin interaction
ENSG00000100445	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10143987	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1043831	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1043839	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158703	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158704	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158705	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158706	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11158707	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11621453	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11621715	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11626161	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11627137	0.81[ASN][1000 genomes]
rs11628143	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12433369	0.90[ASN][1000 genomes]
rs12433402	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12879887	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12882878	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12897925	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1473725	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951123	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1956896	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1956898	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1956899	0.85[EUR][1000 genomes]
rs1956901	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1956903	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1956904	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273628	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277489	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2332333	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332334	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3211056	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4278673	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4290409	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4400972	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4433735	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4981518	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981519	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981521	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981522	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981523	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981524	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4982913	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4982914	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4982916	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4982917	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4982918	0.80[ASN][1000 genomes]
rs4982919	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4982920	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712487	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7143327	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7144118	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7148891	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7149743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151530	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737248	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8015535	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs966493	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1053330	chr14:24908047-24993666	Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	n/a
4	nsv564061	chr14:24911138-24945331	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	n/a
5	esv2761824	chr14:24914008-24993666	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
6	nsv1043355	chr14:24914008-24993666	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
7	nsv1045732	chr14:24914008-25019317	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
8	esv19772	chr14:24914740-24951857	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
9	nsv523200	chr14:24915383-24975032	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
10	nsv521915	chr14:24915383-24992619	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
11	nsv564062	chr14:24915383-24992619	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
12	nsv1039955	chr14:24927313-24993666	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
13	esv3431393	chr14:24929160-24929614	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1956893	SDR39U1	cis	Muscle Skeletal	GTEx
rs1956893	C14orf124	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24912800-24950800	Weak transcription	Gastric	stomach
2	chr14:24913000-24930000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr14:24913000-24931600	Weak transcription	Fetal Kidney	kidney
4	chr14:24913000-24932400	Weak transcription	Primary B cells from cord blood	blood
5	chr14:24913000-24932800	Weak transcription	Primary T cells from cord blood	blood
6	chr14:24922200-24946000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr14:24922800-24951000	Weak transcription	Pancreas	Pancrea
8	chr14:24923200-24937400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:24923600-24932600	Weak transcription	Right Ventricle	heart
10	chr14:24924000-24929400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:24924200-24932000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:24925200-24929600	Weak transcription	Fetal Stomach	stomach
13	chr14:24925800-24933400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:24926000-24936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:24926200-24929400	Weak transcription	Ovary	ovary
16	chr14:24926400-24929600	Weak transcription	Aorta	Aorta
17	chr14:24926400-24930800	Weak transcription	Fetal Intestine Small	intestine
18	chr14:24926400-24934200	Weak transcription	Lung	lung
19	chr14:24926800-24929800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr14:24927600-24930400	Weak transcription	Esophagus	oesophagus
21	chr14:24927600-24951000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:24927800-24929400	Enhancers	Fetal Muscle Leg	muscle
23	chr14:24928200-24934400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:24928200-24950400	Weak transcription	HepG2	liver
25	chr14:24928400-24936000	Weak transcription	Liver	Liver
26	chr14:24928600-24951000	Weak transcription	Placenta	Placenta
27	chr14:24928800-24951000	Weak transcription	Spleen	Spleen

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