Variant report

Variant	rs17409544
Chromosome Location	chr5:80315366-80315367
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11744295	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12152989	1.00[JPT][hapmap]
rs12153055	1.00[JPT][hapmap]
rs13176380	1.00[JPT][hapmap]
rs13177252	1.00[JPT][hapmap]
rs13182907	0.82[JPT][hapmap]
rs16878325	0.95[YRI][hapmap]
rs4704695	1.00[JPT][hapmap]
rs6879497	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
4	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv4897	chr5:80284196-80330223	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80300400-80316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:80300400-80318400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:80303000-80318200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:80305200-80318200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr5:80309800-80317000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr5:80311000-80317400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:80311600-80323800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:80311600-80325400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr5:80312000-80315800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:80312200-80316200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:80312200-80316400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:80312200-80323600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:80312800-80315400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:80312800-80320000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:80313200-80316400	Weak transcription	Fetal Stomach	stomach
16	chr5:80313400-80316600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:80313400-80318200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:80313400-80319400	Weak transcription	Brain Angular Gyrus	brain
19	chr5:80313600-80318400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:80314200-80315400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:80314200-80315600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:80314200-80315600	Enhancers	Brain Substantia Nigra	brain
23	chr5:80314400-80315400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:80314400-80315400	Weak transcription	Primary T cells from cord blood	blood
25	chr5:80314400-80316600	Weak transcription	Brain Hippocampus Middle	brain
26	chr5:80314400-80318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:80314400-80320800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:80314600-80316200	Weak transcription	HMEC	breast
29	chr5:80314600-80316600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:80315000-80316000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:80315000-80316000	Enhancers	Fetal Lung	lung
32	chr5:80315200-80315600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:80315200-80316200	Weak transcription	Placenta	Placenta
34	chr5:80315200-80316400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:80315200-80316600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr5:80315200-80317600	Weak transcription	HepG2	liver
37	chr5:80315200-80317800	Weak transcription	Left Ventricle	heart
38	chr5:80315200-80319800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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