Variant report

Variant	rs17152043
Chromosome Location	chr7:25659427-25659428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10235998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11973866	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11978307	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12534245	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12667261	0.82[ASN][1000 genomes]
rs12670768	0.91[JPT][hapmap]
rs1502948	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873895	0.91[JPT][hapmap]
rs17152030	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17152036	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17152054	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17152061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1818146	0.91[JPT][hapmap]
rs2134479	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2214240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28723687	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960821	0.91[JPT][hapmap]
rs62454635	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73085996	0.84[ASN][1000 genomes]
rs975369	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv1020230	chr7:25649344-25783071	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv2753233	chr7:25655060-25771160	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17152043	DFNA5	cis	lymphoblastoid	seeQTL
rs17152043	TAX1BP1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25653400-25659600	Enhancers	Primary B cells from peripheral blood	blood
2	chr7:25655200-25659600	Weak transcription	Fetal Stomach	stomach
3	chr7:25655200-25660000	Weak transcription	Placenta	Placenta
4	chr7:25655200-25664800	Weak transcription	Fetal Kidney	kidney
5	chr7:25655600-25659600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:25655600-25660000	Weak transcription	Aorta	Aorta
7	chr7:25655600-25664200	Weak transcription	Right Atrium	heart
8	chr7:25655800-25659600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:25655800-25659600	Weak transcription	Fetal Thymus	thymus
10	chr7:25655800-25659800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:25655800-25660200	Weak transcription	Spleen	Spleen
12	chr7:25655800-25660400	Weak transcription	Left Ventricle	heart
13	chr7:25656600-25659600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:25656600-25664200	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:25657000-25665000	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:25657200-25659600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:25657200-25659800	Weak transcription	Fetal Heart	heart
18	chr7:25657400-25659600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr7:25657400-25660000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr7:25657400-25660200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:25657400-25660200	Weak transcription	Small Intestine	intestine
22	chr7:25657400-25664200	Weak transcription	Psoas Muscle	Psoas
23	chr7:25657600-25660200	Weak transcription	Adipose Nuclei	Adipose
24	chr7:25657600-25663600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:25657800-25659800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:25658200-25659600	Enhancers	Primary T cells from cord blood	blood
27	chr7:25658400-25659600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:25658400-25661600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr7:25658600-25659600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr7:25658600-25659600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr7:25658600-25659800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr7:25658600-25660800	Enhancers	Fetal Brain Male	brain
33	chr7:25658800-25659600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr7:25658800-25659800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr7:25658800-25660200	Enhancers	Fetal Brain Female	brain
36	chr7:25659000-25660000	Active TSS	Thymus	Thymus
37	chr7:25659000-25660800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr7:25659000-25661400	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr7:25659200-25659800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr7:25659200-25660400	Enhancers	Fetal Lung	lung
41	chr7:25659400-25659800	Active TSS	Primary B cells from cord blood	blood

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