Variant report

Variant	rs2517563
Chromosome Location	chr6:30598716-30598717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30598484-30598728	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30591157..30598732-chr6:30607879..30619621,21	K562	blood:
2	chr6:30594543..30596206-chr6:30598206..30601181,2	MCF-7	breast:

Variant related genes	Relation type
PTMAP1	TF binding region
ENSG00000137343	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000204564	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1264422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1264442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs14350	1.00[EUR][1000 genomes]
rs17195432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2252845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2394393	1.00[EUR][1000 genomes]
rs2429643	1.00[EUR][1000 genomes]
rs2517562	1.00[EUR][1000 genomes]
rs2517567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2534688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844707	1.00[EUR][1000 genomes]
rs3094103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3094107	1.00[EUR][1000 genomes]
rs3129999	1.00[EUR][1000 genomes]
rs3130674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130675	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132593	1.00[AMR][1000 genomes]
rs34377509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262167	0.83[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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30593600-30613800	Weak transcription	Hela-S3	cervix
2	chr6:30595000-30601200	Weak transcription	Aorta	Aorta
3	chr6:30595200-30599400	Weak transcription	K562	blood
4	chr6:30595200-30601000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:30595200-30601200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:30595200-30607000	Weak transcription	Right Atrium	heart
7	chr6:30595200-30609000	Weak transcription	Colonic Mucosa	Colon
8	chr6:30595400-30601400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:30595400-30607800	Weak transcription	Right Ventricle	heart
10	chr6:30595400-30608200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:30595400-30608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:30595400-30614000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:30595400-30614800	Weak transcription	Small Intestine	intestine
14	chr6:30595600-30599400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:30595600-30600800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:30595600-30600800	Weak transcription	Left Ventricle	heart
17	chr6:30595600-30600800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:30595600-30601000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:30595600-30601200	Weak transcription	Adipose Nuclei	Adipose
20	chr6:30595600-30601200	Weak transcription	Esophagus	oesophagus
21	chr6:30595600-30601200	Weak transcription	Gastric	stomach
22	chr6:30595600-30601200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:30595600-30601200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:30595600-30601200	Weak transcription	HMEC	breast
25	chr6:30595600-30601200	Weak transcription	NHDF-Ad	bronchial
26	chr6:30595600-30601400	Weak transcription	NH-A	brain
27	chr6:30595600-30605200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:30595600-30608000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:30595600-30608200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:30595600-30608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:30595600-30611000	Weak transcription	Primary B cells from cord blood	blood
32	chr6:30595600-30613000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:30595600-30613800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:30595600-30614200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr6:30595600-30614200	Strong transcription	Fetal Stomach	stomach
36	chr6:30595600-30614200	Weak transcription	Psoas Muscle	Psoas
37	chr6:30595600-30614400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:30595800-30598800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr6:30595800-30600200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr6:30595800-30600200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:30595800-30601000	Weak transcription	A549	lung
42	chr6:30595800-30601200	Weak transcription	Pancreas	Pancrea
43	chr6:30595800-30601200	Weak transcription	Stomach Mucosa	stomach
44	chr6:30595800-30601800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:30595800-30602000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:30595800-30602000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:30595800-30602000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:30595800-30602200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:30595800-30602400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:30595800-30602400	Strong transcription	Fetal Intestine Large	intestine

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