Variant report

Variant	rs6861566
Chromosome Location	chr5:50058243-50058244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10053011	1.00[EUR][1000 genomes]
rs2354535	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34653722	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57674462	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59087322	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59260728	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59696604	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61302972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450423	1.00[EUR][1000 genomes]
rs6861235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6862932	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6894122	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73104834	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73104836	1.00[EUR][1000 genomes]
rs7700920	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723019	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7728126	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv598112	chr5:49989701-50062611	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv462164	chr5:50017724-50063035	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv598115	chr5:50017724-50063035	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50039200-50067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:50040000-50069200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:50040400-50059600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:50041400-50058400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:50041400-50068800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:50041800-50069200	Weak transcription	Adipose Nuclei	Adipose
7	chr5:50041800-50070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:50041800-50090000	Weak transcription	Small Intestine	intestine
9	chr5:50046600-50068600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:50047200-50059600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:50047400-50069000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:50047800-50069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:50050000-50059600	Weak transcription	Left Ventricle	heart
14	chr5:50051200-50084600	Weak transcription	NHEK	skin
15	chr5:50051600-50068800	Weak transcription	Fetal Lung	lung
16	chr5:50052000-50078000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:50052200-50067800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:50052600-50069200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:50052800-50098800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:50053400-50058800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:50053800-50059400	Weak transcription	Primary T cells from cord blood	blood
22	chr5:50054200-50059800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:50054400-50069400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr5:50054800-50062400	Weak transcription	HMEC	breast
25	chr5:50055600-50059800	Weak transcription	GM12878-XiMat	blood
26	chr5:50055800-50065200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:50056200-50059200	Weak transcription	Liver	Liver
28	chr5:50056200-50061200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:50056200-50062400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:50056400-50059600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:50056400-50061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:50056600-50062800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:50056600-50063000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:50056600-50070000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:50056800-50064200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:50056800-50067800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:50057000-50059200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr5:50057000-50059400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:50057200-50067400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:50057400-50060400	Strong transcription	Dnd41	blood
42	chr5:50057400-50060600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:50057400-50061800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:50057400-50064000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr5:50057600-50058400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr5:50057600-50059000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:50057600-50059400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:50057600-50060200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:50057600-50065000	Strong transcription	Primary B cells from cord blood	blood
50	chr5:50057800-50058800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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