Variant report

Variant	rs17482660
Chromosome Location	chr13:52727492-52727493
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52718895..52720527-chr13:52725427..52728131,2	MCF-7	breast:
2	chr13:52725842..52728742-chr13:52731896..52733455,2	MCF-7	breast:
3	chr13:52726747..52729442-chr13:52731857..52734601,2	K562	blood:
4	chr13:52714165..52716732-chr13:52726469..52728185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136098	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1000892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12870757	0.81[AMR][1000 genomes]
rs17404248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17482550	1.00[AMR][1000 genomes]
rs17536694	0.88[AMR][1000 genomes]
rs1886540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1886541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34288155	0.89[AMR][1000 genomes]
rs34326189	0.83[AMR][1000 genomes]
rs35302368	0.81[AMR][1000 genomes]
rs35370885	0.89[AMR][1000 genomes]
rs35703449	0.81[AMR][1000 genomes]
rs4438196	0.81[AMR][1000 genomes]
rs4943055	1.00[EUR][1000 genomes]
rs4943065	0.85[AMR][1000 genomes]
rs55969405	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57604069	0.92[AMR][1000 genomes]
rs59763550	0.85[AMR][1000 genomes]
rs59924615	0.85[AMR][1000 genomes]
rs61247071	0.81[AMR][1000 genomes]
rs71437831	0.81[AMR][1000 genomes]
rs7317742	0.85[AMR][1000 genomes]
rs7320155	0.89[AMR][1000 genomes]
rs7325357	0.85[AMR][1000 genomes]
rs7332381	0.85[AMR][1000 genomes]
rs7338832	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73500202	0.92[AMR][1000 genomes]
rs73502304	0.92[AMR][1000 genomes]
rs73502323	0.85[AMR][1000 genomes]
rs7400215	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 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	chr13:52703600-52730800	Weak transcription	Stomach Mucosa	stomach
2	chr13:52703600-52731000	Weak transcription	Brain Angular Gyrus	brain
3	chr13:52703600-52732600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:52703600-52732800	Weak transcription	Psoas Muscle	Psoas
5	chr13:52703600-52733000	Weak transcription	Esophagus	oesophagus
6	chr13:52703800-52731200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:52703800-52731400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:52703800-52731400	Weak transcription	Spleen	Spleen
9	chr13:52703800-52732600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr13:52703800-52732600	Weak transcription	HMEC	breast
11	chr13:52703800-52733200	Weak transcription	Gastric	stomach
12	chr13:52704000-52733000	Weak transcription	Fetal Thymus	thymus
13	chr13:52704800-52730000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr13:52706200-52731000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:52706600-52730800	Weak transcription	HUVEC	blood vessel
16	chr13:52706600-52731000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr13:52706600-52732600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:52706600-52732800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:52706600-52732800	Weak transcription	Pancreas	Pancrea
20	chr13:52707400-52731200	Weak transcription	Primary B cells from cord blood	blood
21	chr13:52707400-52732800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:52707600-52731600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr13:52707600-52732600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:52707800-52732600	Weak transcription	A549	lung
25	chr13:52708000-52732600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr13:52708400-52732600	Weak transcription	HSMMtube	muscle
27	chr13:52708400-52732800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr13:52710400-52732800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr13:52712200-52733000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:52712400-52733000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:52720800-52728600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:52720800-52732400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:52721800-52732600	Weak transcription	NHEK	skin
34	chr13:52723000-52732600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr13:52723000-52732600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:52724000-52731000	Weak transcription	Fetal Intestine Small	intestine
37	chr13:52724200-52732800	Weak transcription	Thymus	Thymus
38	chr13:52725400-52732600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:52725600-52728800	Weak transcription	Small Intestine	intestine
40	chr13:52725600-52731200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:52725800-52731000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr13:52725800-52732600	Weak transcription	Brain Germinal Matrix	brain
43	chr13:52725800-52732600	Weak transcription	Fetal Brain Female	brain
44	chr13:52725800-52732800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:52725800-52732800	Weak transcription	Ovary	ovary
46	chr13:52726000-52728800	Weak transcription	Fetal Stomach	stomach
47	chr13:52726000-52729400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:52726000-52730400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr13:52726000-52730400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr13:52726000-52730400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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