Variant report

Variant	rs16872653
Chromosome Location	chr6:12324483-12324484
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:12012173..12014577-chr6:12323269..12325168,2	MCF-7	breast:
2	chr6:12286229..12288972-chr6:12321405..12325827,4	MCF-7	breast:
3	chr6:12299143..12301342-chr6:12323283..12325161,2	MCF-7	breast:
4	chr6:12315560..12317298-chr6:12323105..12324683,2	MCF-7	breast:
5	chr6:12322236..12325054-chr6:12326610..12329434,2	K562	blood:
6	chr6:12320054..12322576-chr6:12323490..12326394,2	MCF-7	breast:
7	chr6:12302992..12304861-chr6:12320967..12324603,3	MCF-7	breast:
8	chr6:12289159..12293070-chr6:12321878..12326678,5	MCF-7	breast:
9	chr6:12323445..12325043-chr6:12354923..12356472,2	MCF-7	breast:
10	chr6:12311114..12311968-chr6:12323955..12324795,2	MCF-7	breast:
11	chr6:12321927..12325444-chr6:12488868..12492076,3	MCF-7	breast:
12	chr6:12289263..12293878-chr6:12323003..12327079,6	MCF-7	breast:
13	chr6:12311955..12317813-chr6:12323964..12327057,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000078401	Chromatin interaction
ENSG00000095951	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16872592	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16872602	0.84[EUR][1000 genomes]
rs16872628	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872650	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872679	0.83[AMR][1000 genomes]
rs6899673	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6906760	0.93[EUR][1000 genomes]
rs7356986	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7760229	0.83[AMR][1000 genomes]
rs9296345	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9471435	0.93[EUR][1000 genomes]
rs9471486	0.83[AMR][1000 genomes]
rs9471496	0.83[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12315200-12327800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:12319200-12324600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:12319400-12325600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:12320000-12324800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:12322400-12325400	Enhancers	Fetal Intestine Large	intestine
6	chr6:12322400-12325400	Enhancers	Fetal Intestine Small	intestine
7	chr6:12322600-12324600	Enhancers	A549	lung
8	chr6:12322600-12325400	Enhancers	HepG2	liver
9	chr6:12323000-12325400	Enhancers	Stomach Mucosa	stomach
10	chr6:12323200-12325800	Enhancers	HMEC	breast
11	chr6:12323400-12327000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:12323600-12325600	Enhancers	HUVEC	blood vessel
13	chr6:12323600-12325800	Enhancers	Hela-S3	cervix
14	chr6:12323800-12324600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:12323800-12328000	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:12324200-12324800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:12324200-12325000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:12324200-12325000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:12324200-12325400	Enhancers	Placenta	Placenta
20	chr6:12324200-12325400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:12324200-12325800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:12324400-12324600	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:12324400-12324800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:12324400-12324800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:12324400-12324800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr6:12324400-12324800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:12324400-12324800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:12324400-12324800	Enhancers	Pancreas	Pancrea
29	chr6:12324400-12324800	Enhancers	Osteobl	bone
30	chr6:12324400-12325200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:12324400-12325200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:12324400-12325200	Enhancers	Duodenum Mucosa	Duodenum
33	chr6:12324400-12325200	Flanking Active TSS	NHEK	skin
34	chr6:12324400-12325400	Enhancers	Primary T cells from cord blood	blood
35	chr6:12324400-12325400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr6:12324400-12325400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:12324400-12325400	Enhancers	NH-A	brain
38	chr6:12324400-12325800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr6:12324400-12326000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr6:12324400-12327000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr6:12324400-12327200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:12324400-12327400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:12324400-12328600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:12324400-12329200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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