Variant report

Variant	rs25527
Chromosome Location	chr6:30690938-30690939
allele	C/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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30687338..30691474-chr6:30850428..30854318,11	MCF-7	breast:
2	chr6:30646431..30647401-chr6:30690082..30691095,13	MCF-7	breast:
3	chr6:30613134..30616889-chr6:30684889..30690956,7	MCF-7	breast:
4	chr6:30689083..30692064-chr6:30851539..30853940,2	K562	blood:
5	chr6:30628328..30630913-chr6:30689339..30690997,2	K562	blood:
6	chr6:30522151..30525852-chr6:30686505..30691954,11	K562	blood:
7	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
8	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
9	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
10	chr6:30646446..30647403-chr6:30689906..30691430,10	K562	blood:
11	chr6:30638422..30642374-chr6:30687329..30691225,7	MCF-7	breast:
12	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
13	chr13:41956378..41959414-chr6:30690779..30694701,5	K562	blood:
14	chr6:30455790..30458568-chr6:30687436..30691942,4	MCF-7	breast:
15	chr6:30646636..30647399-chr6:30690429..30691049,3	MCF-7	breast:
16	chr6:30652479..30653370-chr6:30690436..30690984,2	K562	blood:
17	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
18	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000214222	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1064627	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2284173	0.99[ASN][1000 genomes]
rs3094127	0.83[ASN][1000 genomes]
rs3095329	0.99[ASN][1000 genomes]
rs3095330	0.83[ASN][1000 genomes]
rs3132584	0.99[ASN][1000 genomes]
rs41270533	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56389899	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8233	0.99[ASN][1000 genomes]
rs9295910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9501029	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970104	chr6:30690935-30693035	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30688200-30692400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr6:30688400-30691800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:30688800-30693200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:30689000-30691000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
5	chr6:30689000-30691800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr6:30689400-30691000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:30689400-30691000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:30689400-30691000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
9	chr6:30689400-30691000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
10	chr6:30689400-30691000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
11	chr6:30689400-30691000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
12	chr6:30689400-30691000	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:30689400-30691000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
14	chr6:30689400-30691200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
15	chr6:30689400-30691200	Transcr. at gene 5' and 3'	A549	lung
16	chr6:30689400-30691200	Transcr. at gene 5' and 3'	K562	blood
17	chr6:30689400-30691600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:30689400-30692000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:30689400-30692000	Transcr. at gene 5' and 3'	HMEC	breast
20	chr6:30689400-30692400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr6:30689400-30692400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:30689400-30692400	Transcr. at gene 5' and 3'	NHLF	lung
23	chr6:30689400-30693000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:30689400-30693000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:30689400-30694000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:30689400-30694000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:30689600-30691000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
28	chr6:30689600-30691000	Transcr. at gene 5' and 3'	Osteobl	bone
29	chr6:30689600-30691600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:30689600-30692200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
31	chr6:30689800-30691000	Transcr. at gene 5' and 3'	HepG2	liver
32	chr6:30689800-30691200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:30689800-30691600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
34	chr6:30690000-30691000	Weak transcription	Aorta	Aorta
35	chr6:30690000-30691400	Weak transcription	Ovary	ovary
36	chr6:30690000-30693000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:30690000-30694000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
38	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:30690200-30691000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
40	chr6:30690200-30691000	Transcr. at gene 5' and 3'	Fetal Heart	heart
41	chr6:30690200-30691200	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
42	chr6:30690200-30692000	Transcr. at gene 5' and 3'	Hela-S3	cervix
43	chr6:30690200-30693000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:30690200-30693400	Transcr. at gene 5' and 3'	NH-A	brain
45	chr6:30690200-30694000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
46	chr6:30690200-30699200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:30690400-30691000	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr6:30690400-30691000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:30690400-30691000	Genic enhancers	Brain Substantia Nigra	brain
50	chr6:30690400-30691000	Transcr. at gene 5' and 3'	Fetal Kidney	kidney

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