Variant report

Variant	rs12199500
Chromosome Location	chr6:54712529-54712530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54659157..54661825-chr6:54711858..54713372,2	MCF-7	breast:
2	chr12:14922583..14923432-chr6:54712365..54712882,2	Hela-S3	cervix:
3	chr6:54562847..54563534-chr6:54712448..54713092,2	MCF-7	breast:
4	chr6:54711853..54714484-chr8:48522444..48524308,2	MCF-7	breast:
5	chr6:54633061..54636995-chr6:54710354..54713223,5	MCF-7	breast:
6	chr6:54709728..54711702-chr6:54712389..54714158,2	K562	blood:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction
ENSG00000197837	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]
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]
rs72954829	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:49 , 50 per page) page: 1

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	chr6:54710800-54712600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:54710800-54712600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:54710800-54712800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:54710800-54713000	Active TSS	Fetal Intestine Small	intestine
10	chr6:54710800-54713000	Active TSS	Right Atrium	heart
11	chr6:54710800-54713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr6:54710800-54714400	Active TSS	Colonic Mucosa	Colon
13	chr6:54711000-54712600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:54711000-54712600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:54711000-54712600	Bivalent/Poised TSS	Fetal Thymus	thymus
16	chr6:54711000-54712800	Active TSS	Fetal Kidney	kidney
17	chr6:54711000-54713200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr6:54711000-54713200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:54711000-54713200	Active TSS	Esophagus	oesophagus
20	chr6:54711000-54713200	Active TSS	Gastric	stomach
21	chr6:54711000-54713400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:54711200-54712600	Active TSS	Fetal Lung	lung
23	chr6:54711200-54713000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:54711200-54713400	Active TSS	NHEK	skin
25	chr6:54711200-54713600	Active TSS	HMEC	breast
26	chr6:54711400-54713200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
27	chr6:54711600-54712600	Enhancers	Liver	Liver
28	chr6:54711600-54713200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr6:54711800-54712600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
30	chr6:54711800-54712800	Bivalent/Poised TSS	Stomach Mucosa	stomach
31	chr6:54711800-54713000	Flanking Active TSS	Placenta	Placenta
32	chr6:54712000-54712600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:54712000-54713200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:54712200-54712600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
35	chr6:54712200-54712800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
36	chr6:54712200-54712800	Bivalent/Poised TSS	Fetal Stomach	stomach
37	chr6:54712200-54712800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
38	chr6:54712200-54713000	Active TSS	Fetal Intestine Large	intestine
39	chr6:54712200-54713600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:54712200-54714400	Flanking Active TSS	Hela-S3	cervix
41	chr6:54712400-54712600	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:54712400-54712600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr6:54712400-54712600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:54712400-54712600	Bivalent/Poised TSS	Small Intestine	intestine
45	chr6:54712400-54712800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:54712400-54712800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
47	chr6:54712400-54712800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:54712400-54712800	Enhancers	Fetal Heart	heart
49	chr6:54712400-54712800	Flanking Active TSS	Pancreas	Pancrea

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