Variant report

Variant	rs2841553
Chromosome Location	chr6:13468103-13468104
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13465251..13472690-chr6:13481619..13489131,10	K562	blood:
2	chr6:13466729..13469720-chr6:13485556..13487664,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000187461	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11964734	0.90[MKK][hapmap];1.00[AMR][1000 genomes]
rs2434393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2434394	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2494771	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560750	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560751	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560752	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560816	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560817	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2560818	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2841554	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2841556	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2841557	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2841558	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2841559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58453010	0.83[AMR][1000 genomes]
rs59772696	1.00[AMR][1000 genomes]
rs6931785	1.00[AMR][1000 genomes]
rs73725831	1.00[AMR][1000 genomes]
rs766773	0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7774411	0.83[AMR][1000 genomes]
rs9382115	0.83[AMR][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS 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
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13452200-13483400	Weak transcription	Gastric	stomach
2	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
3	chr6:13455200-13484400	Weak transcription	Small Intestine	intestine
4	chr6:13455200-13484600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:13455400-13481000	Weak transcription	HUVEC	blood vessel
6	chr6:13462600-13470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:13462800-13484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:13463000-13468200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr6:13463000-13468200	Enhancers	Psoas Muscle	Psoas
10	chr6:13463000-13470800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:13463200-13468800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:13463200-13481000	Weak transcription	A549	lung
13	chr6:13463400-13476600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:13463600-13470200	Weak transcription	Osteobl	bone
15	chr6:13463600-13470400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:13463600-13470600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:13463600-13473200	Weak transcription	HepG2	liver
18	chr6:13463600-13484400	Weak transcription	Primary T cells from cord blood	blood
19	chr6:13463800-13484600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:13464600-13468600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:13464600-13469000	Weak transcription	Lung	lung
22	chr6:13464600-13469200	Weak transcription	Brain Substantia Nigra	brain
23	chr6:13464600-13470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:13464600-13476400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:13464800-13468800	Weak transcription	Aorta	Aorta
26	chr6:13465200-13485000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:13465800-13468200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:13465800-13470200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:13466000-13470200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:13466200-13468400	Enhancers	Brain Angular Gyrus	brain
31	chr6:13466200-13470400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:13466200-13470400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:13466200-13470400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:13466200-13470800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:13466400-13470200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:13466400-13470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:13466400-13470400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:13466400-13473400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:13466600-13468200	Enhancers	Pancreas	Pancrea
40	chr6:13466600-13468200	Enhancers	K562	blood
41	chr6:13466600-13470200	Enhancers	Brain Cingulate Gyrus	brain
42	chr6:13466600-13470400	Weak transcription	NH-A	brain
43	chr6:13466800-13468600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:13466800-13469000	Genic enhancers	Left Ventricle	heart
45	chr6:13466800-13474200	Weak transcription	Hela-S3	cervix
46	chr6:13467000-13469800	Weak transcription	NHEK	skin
47	chr6:13467000-13470400	Weak transcription	Right Ventricle	heart
48	chr6:13467000-13478600	Weak transcription	Thymus	Thymus
49	chr6:13467200-13468200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:13467200-13468800	Weak transcription	Right Atrium	heart

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