Variant report

Variant	rs58936409
Chromosome Location	chr17:17807235-17807236
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17806459..17808232-chr17:17813568..17815974,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs16960767	1.00[AMR][1000 genomes]
rs16960818	1.00[AMR][1000 genomes]
rs56054716	1.00[AMR][1000 genomes]
rs56153053	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56160247	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56232485	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56928492	1.00[AMR][1000 genomes]
rs57082481	1.00[AMR][1000 genomes]
rs57134764	1.00[EUR][1000 genomes]
rs57277459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57791826	1.00[AMR][1000 genomes]
rs58116638	1.00[EUR][1000 genomes]
rs58219643	1.00[AMR][1000 genomes]
rs58376085	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58676524	1.00[AMR][1000 genomes]
rs58970292	1.00[EUR][1000 genomes]
rs61050785	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61060916	1.00[AMR][1000 genomes]
rs61188141	1.00[AMR][1000 genomes]
rs61256737	1.00[AMR][1000 genomes]
rs7218054	1.00[AMR][1000 genomes]
rs7218246	1.00[AMR][1000 genomes]
rs7218594	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221934	1.00[AMR][1000 genomes]
rs7224621	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297834	1.00[AMR][1000 genomes]
rs73297855	1.00[AMR][1000 genomes]
rs73297868	1.00[AMR][1000 genomes]
rs73299861	1.00[AMR][1000 genomes]
rs73299873	1.00[AMR][1000 genomes]
rs73299892	1.00[AMR][1000 genomes]
rs73301827	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73301859	1.00[AMR][1000 genomes]
rs73301894	1.00[AMR][1000 genomes]
rs73303812	1.00[AMR][1000 genomes]
rs73303813	1.00[AMR][1000 genomes]
rs73303833	1.00[AMR][1000 genomes]
rs73303840	1.00[EUR][1000 genomes]
rs73303844	1.00[EUR][1000 genomes]
rs73303854	1.00[AMR][1000 genomes]
rs73303856	1.00[AMR][1000 genomes]
rs73303857	1.00[AMR][1000 genomes]
rs73305952	1.00[AMR][1000 genomes]
rs73979211	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979217	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73979243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73981076	1.00[AMR][1000 genomes]
rs8066528	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066865	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8067146	1.00[EUR][1000 genomes]
rs8068860	1.00[EUR][1000 genomes]
rs8078368	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078811	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9914362	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
7	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17767600-17807400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:17781600-17810600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:17782200-17817000	Weak transcription	Fetal Kidney	kidney
4	chr17:17783000-17808200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr17:17793000-17817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:17797000-17817000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:17797600-17822400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:17800800-17807800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:17801200-17817200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:17802400-17817000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:17802600-17808200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr17:17802600-17817600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:17802600-17820000	Weak transcription	Primary B cells from cord blood	blood
14	chr17:17802600-17822400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:17802800-17808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:17802800-17812400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr17:17803000-17808000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr17:17803000-17810200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:17803200-17808800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:17803400-17807800	Enhancers	Fetal Heart	heart
21	chr17:17804400-17808000	Weak transcription	Aorta	Aorta
22	chr17:17804600-17807800	Weak transcription	Fetal Intestine Large	intestine
23	chr17:17804600-17808000	Enhancers	Adipose Nuclei	Adipose
24	chr17:17804600-17808200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr17:17804600-17810000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:17804600-17810400	Weak transcription	Fetal Brain Male	brain
27	chr17:17804800-17807800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:17804800-17807800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:17804800-17808000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr17:17804800-17808000	Weak transcription	Brain Germinal Matrix	brain
31	chr17:17804800-17808000	Weak transcription	NHEK	skin
32	chr17:17804800-17808200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:17804800-17810000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr17:17804800-17810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:17804800-17814000	Weak transcription	Fetal Thymus	thymus
36	chr17:17804800-17814600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:17805000-17807400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:17805000-17807800	Weak transcription	Brain Angular Gyrus	brain
39	chr17:17805000-17808000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr17:17805000-17808000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:17805000-17808000	Weak transcription	Pancreas	Pancrea
42	chr17:17805000-17808000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr17:17805000-17808200	Weak transcription	Brain Hippocampus Middle	brain
44	chr17:17805000-17808200	Genic enhancers	Fetal Muscle Leg	muscle
45	chr17:17805000-17808200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr17:17805000-17808400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:17805000-17809800	Weak transcription	HUVEC	blood vessel
48	chr17:17805000-17810000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:17805000-17810000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr17:17805000-17810400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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