Variant report

Variant	rs9654578
Chromosome Location	chr6:25140405-25140406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:25140377-25140427	Caco-2	colon:	n/a
2	chr6:25140377-25140427	BJ	skin:	n/a
3	chr6:25140377-25140427	HRPEpiC	eye:	n/a
4	chr6:25140377-25140427	GM12892	blood:	n/a
5	chr6:25140377-25140427	H1-hESC	embryonic stem cell:	embryo
6	chr6:25140377-25140427	HCT-116	colon:	n/a
7	chr6:25140377-25140427	ovcar-3	ovarian:	n/a
8	chr6:25140377-25140427	HAEpiC	amniotic membrane:	n/a
9	chr6:25140377-25140427	SK-N-SH_RA	brain:	n/a
10	chr6:25140377-25140427	PANC-1	pancreas:	n/a
11	chr6:25140377-25140427	T-47D	breast:	n/a
12	chr6:25140377-25140427	HIPEpiC	eye:	n/a
13	chr6:25140377-25140427	HCF	heart:	n/a
14	chr6:25140377-25140427	U87	brain:	n/a
15	chr6:25140377-25140427	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:25140377-25140427	SK-N-MC	brain:	n/a
17	chr6:25140377-25140427	HRCEpiC	kidney:	n/a
18	chr6:25140377-25140427	HCPEpiC	choroid plexus:	n/a
19	chr6:25140377-25140427	AG09319	gingival:	n/a
20	chr6:25140377-25140427	Hepatocyte	liver:	n/a
21	chr6:25140377-25140427	SK-N-SH	brain:	n/a
22	chr6:25140377-25140427	CMK	blood:	n/a
23	chr6:25140377-25140427	NHBE	bronchial:	n/a
24	chr6:25140377-25140427	HEK293	kidney:	embryo
25	chr6:25140377-25140427	HL-60	blood:	n/a
26	chr6:25140377-25140427	HMEC	breast:	n/a
27	chr6:25140377-25140427	Jurkat	blood:	n/a
28	chr6:25140377-25140427	HCM	heart:	n/a
29	chr6:25140377-25140427	HRE	kidney:	n/a
30	chr6:25140377-25140427	PrEC	prostate:	n/a
31	chr6:25140377-25140427	PFSK-1	brain:	n/a
32	chr6:25140377-25140427	IMR90	lung:	fetal
33	chr6:25140377-25140427	SKMC	muscle:	n/a
34	chr6:25140377-25140427	NB4	blood:	n/a
35	chr6:25140377-25140427	BE2_C	brain:	n/a
36	chr6:25140377-25140427	AG04450	lung:	fetal
37	chr6:25140377-25140427	MCF10A-Er-Src	breast:	n/a
38	chr6:25140377-25140427	ProgFib	skin:	n/a
39	chr6:25140377-25140427	LNCaP	prostate:	n/a
40	chr6:25140377-25140427	HNPCEpiC	eye:	n/a
41	chr6:25140377-25140427	NH-A	brain:	n/a
42	chr6:25140377-25140427	ECC-1	luminal epithelium:	n/a
43	chr6:25140377-25140427	HEEpiC	esophagus:	n/a
44	chr6:25140377-25140427	RPTEC	kidney:	n/a
45	chr6:25140377-25140427	AoSMC	blood vessel:	n/a
46	chr6:25140377-25140427	SAEC	small airway:	n/a
47	chr6:25140377-25140427	A549	lung:	n/a
48	chr6:25140377-25140427	GM12891	blood:	n/a
49	chr6:25140377-25140427	NHDF-neo	bronchial:	n/a
50	chr6:25140377-25140427	K562	blood:	n/a

No data

Variant related genes	Relation type
CMAHP	CpG island

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs182499	0.86[ASN][1000 genomes]
rs188567	1.00[ASN][1000 genomes]
rs28539031	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302981	1.00[ASN][1000 genomes]
rs303003	0.86[ASN][1000 genomes]
rs303012	0.86[ASN][1000 genomes]
rs416030	0.86[ASN][1000 genomes]
rs55851821	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908916	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386265	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73386299	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv969354	chr6:25139819-25141640	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25138800-25152800	Weak transcription	Lung	lung
2	chr6:25139200-25154800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:25139600-25140600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:25139600-25141800	Weak transcription	Fetal Thymus	thymus
5	chr6:25139600-25152800	Weak transcription	Thymus	Thymus
6	chr6:25139800-25140800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:25140000-25140600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:25140000-25140600	Enhancers	Dnd41	blood
9	chr6:25140000-25142600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:25140000-25143000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:25140000-25146800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:25140000-25146800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:25140000-25146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25140200-25142800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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