Variant report

Variant	rs72954829
Chromosome Location	chr6:54711786-54711787
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57504760..57505339-chr6:54711585..54712336,2	Hela-S3	cervix:
2	chr14:65876592..65878564-chr6:54710365..54711981,2	MCF-7	breast:
3	chr15:31283483..31284320-chr6:54711525..54712159,2	Hela-S3	cervix:
4	chr6:54633061..54636995-chr6:54710354..54713223,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000033170	Chromatin interaction
ENSG00000220635	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10807486	0.82[EUR][1000 genomes]
rs12199500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12203166	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12203906	0.90[AMR][1000 genomes]
rs12203996	0.90[AMR][1000 genomes]
rs12205593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12211620	1.00[AMR][1000 genomes]
rs72954818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72954824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72954849	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72954852	0.90[EUR][1000 genomes]
rs72957593	0.90[AMR][1000 genomes]
rs7744880	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr6:54710400-54713200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:54710600-54713800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:54710800-54712200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:54710800-54712200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
8	chr6:54710800-54712400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr6:54710800-54712400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:54710800-54712400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:54710800-54712600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:54710800-54712600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:54710800-54712800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:54710800-54713000	Active TSS	Fetal Intestine Small	intestine
15	chr6:54710800-54713000	Active TSS	Right Atrium	heart
16	chr6:54710800-54713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:54710800-54714400	Active TSS	Colonic Mucosa	Colon
18	chr6:54711000-54711800	Active TSS	Stomach Mucosa	stomach
19	chr6:54711000-54711800	Bivalent/Poised TSS	NHLF	lung
20	chr6:54711000-54712000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:54711000-54712000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:54711000-54712000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:54711000-54712000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:54711000-54712000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:54711000-54712000	Bivalent/Poised TSS	A549	lung
26	chr6:54711000-54712000	Active TSS	NH-A	brain
27	chr6:54711000-54712000	Bivalent/Poised TSS	Osteobl	bone
28	chr6:54711000-54712200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:54711000-54712200	Bivalent/Poised TSS	Fetal Brain Female	brain
30	chr6:54711000-54712200	Active TSS	Fetal Heart	heart
31	chr6:54711000-54712200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
32	chr6:54711000-54712200	Bivalent/Poised TSS	Psoas Muscle	Psoas
33	chr6:54711000-54712200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr6:54711000-54712200	Bivalent/Poised TSS	Thymus	Thymus
35	chr6:54711000-54712200	Active TSS	Hela-S3	cervix
36	chr6:54711000-54712400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:54711000-54712400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
38	chr6:54711000-54712400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:54711000-54712400	Active TSS	Pancreas	Pancrea
40	chr6:54711000-54712400	Active TSS	Small Intestine	intestine
41	chr6:54711000-54712600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:54711000-54712600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr6:54711000-54712600	Bivalent/Poised TSS	Fetal Thymus	thymus
44	chr6:54711000-54712800	Active TSS	Fetal Kidney	kidney
45	chr6:54711000-54713200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr6:54711000-54713200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:54711000-54713200	Active TSS	Esophagus	oesophagus
48	chr6:54711000-54713200	Active TSS	Gastric	stomach
49	chr6:54711000-54713400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr6:54711200-54711800	Active TSS	H1 Cell Line	embryonic stem cell

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