Variant report

Variant	rs28594674
Chromosome Location	chr6:27203739-27203740
allele	A/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27202802..27205636-chr6:27246312..27248576,2	K562	blood:
2	chr6:27202945..27207226-chr6:27207417..27209319,3	MCF-7	breast:
3	chr6:27203220..27205939-chr6:27245296..27248944,5	K562	blood:
4	chr6:27203165..27205210-chr6:27218359..27220462,2	MCF-7	breast:
5	chr6:27112894..27116381-chr6:27203739..27206608,3	K562	blood:
6	chr6:27197426..27201736-chr6:27203200..27207154,7	K562	blood:
7	chr6:27192628..27195388-chr6:27203355..27206168,2	K562	blood:
8	chr6:27202839..27205784-chr6:27218502..27221340,2	MCF-7	breast:
9	chr6:27202749..27204748-chr6:27656090..27658081,2	K562	blood:
10	chr6:27195411..27200167-chr6:27200252..27206108,10	K562	blood:
11	chr6:27203282..27204812-chr6:27256715..27259261,2	K562	blood:
12	chr6:27202793..27205755-chr6:27355430..27357171,2	K562	blood:
13	chr6:27203048..27205771-chr6:27439622..27441138,2	K562	blood:
14	chr6:27201796..27205755-chr6:27355401..27357171,3	K562	blood:
15	chr6:27112894..27115278-chr6:27203418..27205239,2	K562	blood:
16	chr6:27129016..27131060-chr6:27203219..27204957,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10946904	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1102563	0.82[AFR][1000 genomes]
rs1156086	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142686	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2295603	0.87[ASN][1000 genomes]
rs3800309	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800314	0.83[ASN][1000 genomes]
rs4236043	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546474	0.87[ASN][1000 genomes]
rs4713072	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713074	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5030956	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902268	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916555	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6917311	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940384	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468009	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468010	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468013	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468015	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs996247	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27199000-27205600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27201400-27203800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27202000-27203800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27202400-27204200	Active TSS	K562	blood
5	chr6:27202600-27203800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:27202600-27203800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27202600-27203800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:27202800-27203800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:27202800-27203800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:27202800-27203800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:27202800-27203800	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr6:27202800-27203800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:27202800-27203800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:27202800-27204000	Enhancers	HepG2	liver
15	chr6:27202800-27204400	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:27202800-27205600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:27203200-27205400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:27203200-27205400	Weak transcription	NHLF	lung
19	chr6:27203400-27203800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:27203400-27203800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:27203400-27205000	Weak transcription	GM12878-XiMat	blood
22	chr6:27203400-27205400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:27203400-27205400	Weak transcription	HUVEC	blood vessel
24	chr6:27203400-27205400	Weak transcription	Osteobl	bone
25	chr6:27203400-27205600	Weak transcription	NHDF-Ad	bronchial
26	chr6:27203400-27205800	Weak transcription	HSMMtube	muscle
27	chr6:27203600-27204000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:27203600-27204200	Weak transcription	A549	lung
29	chr6:27203600-27205000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:27203600-27205000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27203600-27205000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:27203600-27205000	Weak transcription	HSMM	muscle
33	chr6:27203600-27205200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:27203600-27205200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:27203600-27205400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:27203600-27205400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:27203600-27205400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:27203600-27205600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:27203600-27205600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:27203600-27205600	Weak transcription	HMEC	breast
41	chr6:27203600-27205600	Weak transcription	NHEK	skin

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