Variant report

Variant	rs72839468
Chromosome Location	chr6:27301734-27301735
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27218055..27220276-chr6:27300325..27303096,3	K562	blood:
2	chr6:27298779..27303006-chr6:27440534..27442735,4	K562	blood:
3	chr6:27299766..27302375-chr6:27444830..27446395,2	K562	blood:
4	chr6:27258451..27260109-chr6:27301059..27302632,2	K562	blood:
5	chr6:27298898..27303175-chr6:27340830..27343404,5	K562	blood:
6	chr6:27287824..27293332-chr6:27295713..27302247,8	K562	blood:
7	chr6:27291413..27293040-chr6:27299829..27302713,2	MCF-7	breast:
8	chr6:27264150..27266831-chr6:27300629..27302449,2	K562	blood:
9	chr6:27300837..27303680-chr6:27307517..27309958,2	K562	blood:
10	chr6:27277495..27280431-chr6:27299498..27302391,2	K562	blood:
11	chr6:27263999..27267440-chr6:27299677..27302604,5	K562	blood:
12	chr6:27276791..27280576-chr6:27298923..27302888,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000112812	Chromatin interaction
ENSG00000158553	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10456051	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10456355	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12189640	0.86[AMR][1000 genomes]
rs12191414	0.94[EUR][1000 genomes]
rs12191649	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12192560	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12193557	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12194341	0.86[AMR][1000 genomes]
rs12194842	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12195783	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12196452	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12196970	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12199685	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12199806	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12202956	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12204953	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12205044	0.86[AMR][1000 genomes]
rs12209174	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12209905	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12211931	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12212348	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12212389	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12212632	0.86[AMR][1000 genomes]
rs12213471	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12213533	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12215289	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12215353	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12215386	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12215878	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12374607	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12374649	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28410967	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62617138	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72839448	1.00[AFR][1000 genomes]
rs72839451	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72839469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72839470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72839471	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72839474	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72839479	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72843151	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72843177	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72843191	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72845208	1.00[AFR][1000 genomes]
rs72845232	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9348763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368509	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9379975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393803	0.81[ASN][1000 genomes]
rs9393814	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2761047	chr6:27296775-27303927	Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27300200-27303200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27300200-27303400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27300400-27301800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:27300400-27301800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:27300400-27302000	Active TSS	GM12878-XiMat	blood
6	chr6:27300400-27302400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:27300400-27303200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:27300400-27303200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:27300400-27303400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:27300400-27303600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:27300600-27301800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:27300600-27302000	Active TSS	K562	blood
13	chr6:27300600-27302200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:27300600-27302200	Active TSS	HMEC	breast
15	chr6:27300800-27301800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:27300800-27301800	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr6:27300800-27301800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:27300800-27302000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:27300800-27302000	Active TSS	A549	lung
20	chr6:27300800-27302000	Active TSS	NHEK	skin
21	chr6:27301400-27301800	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
22	chr6:27301400-27301800	Active TSS	HUVEC	blood vessel
23	chr6:27301400-27321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:27301600-27301800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:27301600-27301800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:27301600-27301800	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:27301600-27301800	Flanking Active TSS	HepG2	liver
28	chr6:27301600-27302000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:27301600-27302200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:27301600-27302400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links