Variant report

Variant	rs588158
Chromosome Location	chr6:4079592-4079593
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr6:4079477-4079596	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr6:4079332-4079671	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:4079509-4079856	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:4079572-4079622	HEEpiC	esophagus:	n/a
2	chr6:4079572-4079622	HL-60	blood:	n/a
3	chr6:4079572-4079622	HAEpiC	amniotic membrane:	n/a
4	chr6:4079572-4079622	HCM	heart:	n/a
5	chr6:4079572-4079622	ovcar-3	ovarian:	n/a
6	chr6:4079572-4079622	K562	blood:	n/a
7	chr6:4079572-4079622	HRCEpiC	kidney:	n/a
8	chr6:4079572-4079622	HCT-116	colon:	n/a
9	chr6:4079572-4079622	HEK293	kidney:	embryo
10	chr6:4079572-4079622	SKMC	muscle:	n/a
11	chr6:4079572-4079622	PrEC	prostate:	n/a
12	chr6:4079572-4079622	RPTEC	kidney:	n/a
13	chr6:4079572-4079622	HRPEpiC	eye:	n/a
14	chr6:4079572-4079622	U87	brain:	n/a
15	chr6:4079572-4079622	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:4079572-4079622	Hepatocyte	liver:	n/a
17	chr6:4079572-4079622	Hela-S3	cervix:	n/a
18	chr6:4079572-4079622	SK-N-MC	brain:	n/a
19	chr6:4079572-4079622	CMK	blood:	n/a
20	chr6:4079572-4079622	SAEC	small airway:	n/a
21	chr6:4079572-4079622	HMEC	breast:	n/a
22	chr6:4079572-4079622	NB4	blood:	n/a
23	chr6:4079572-4079622	BE2_C	brain:	n/a
24	chr6:4079572-4079622	T-47D	breast:	n/a
25	chr6:4079572-4079622	SK-N-SH_RA	brain:	n/a
26	chr6:4079572-4079622	MCF-7	breast:	n/a
27	chr6:4079572-4079622	NHDF-neo	bronchial:	n/a
28	chr6:4079572-4079622	HRE	kidney:	n/a
29	chr6:4079572-4079622	Caco-2	colon:	n/a
30	chr6:4079572-4079622	GM19239	blood:	n/a
31	chr6:4079572-4079622	AG09309	skin:	n/a
32	chr6:4079572-4079622	PANC-1	pancreas:	n/a
33	chr6:4079572-4079622	MCF10A-Er-Src	breast:	n/a
34	chr6:4079572-4079622	LNCaP	prostate:	n/a
35	chr6:4079572-4079622	NHBE	bronchial:	n/a
36	chr6:4079572-4079622	ECC-1	luminal epithelium:	n/a
37	chr6:4079572-4079622	AG09319	gingival:	n/a
38	chr6:4079572-4079622	SK-N-SH	brain:	n/a
39	chr6:4079572-4079622	BJ	skin:	n/a
40	chr6:4079572-4079622	HepG2	liver:	n/a
41	chr6:4079572-4079622	ProgFib	skin:	n/a
42	chr6:4079572-4079622	GM12892	blood:	n/a
43	chr6:4079572-4079622	H1-hESC	embryonic stem cell:	embryo
44	chr6:4079572-4079622	AG10803	skin:	n/a
45	chr6:4079572-4079622	IMR90	lung:	fetal
46	chr6:4079572-4079622	AG04450	lung:	fetal
47	chr6:4079572-4079622	HCF	heart:	n/a
48	chr6:4079572-4079622	GM12878	blood:	n/a
49	chr6:4079572-4079622	A549	lung:	n/a
50	chr6:4079572-4079622	Jurkat	blood:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-4	chr6:4079440-4079914	NR_104464
2	lnc-C6orf201-4	chr6:4076360-4079955	NONHSAT107293

No data

Variant related genes	Relation type
FAM217A	TF binding region
FAM217A	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs101418	0.87[ASN][1000 genomes]
rs11755877	0.87[ASN][1000 genomes]
rs1204951	0.85[ASN][1000 genomes]
rs2473597	0.87[ASN][1000 genomes]
rs2745453	0.87[ASN][1000 genomes]
rs2745455	0.87[ASN][1000 genomes]
rs2783063	0.86[ASN][1000 genomes]
rs589494	0.81[ASN][1000 genomes]
rs590675	0.87[ASN][1000 genomes]
rs592953	0.87[ASN][1000 genomes]
rs593291	0.86[ASN][1000 genomes]
rs594662	0.87[ASN][1000 genomes]
rs595413	0.87[ASN][1000 genomes]
rs608195	0.84[ASN][1000 genomes]
rs609946	0.87[ASN][1000 genomes]
rs612477	0.84[ASN][1000 genomes]
rs617604	0.86[ASN][1000 genomes]
rs619483	0.87[ASN][1000 genomes]
rs620901	0.86[ASN][1000 genomes]
rs627259	0.84[ASN][1000 genomes]
rs634114	0.87[ASN][1000 genomes]
rs639905	0.87[ASN][1000 genomes]
rs651246	0.87[ASN][1000 genomes]
rs653431	0.87[ASN][1000 genomes]
rs654621	0.87[ASN][1000 genomes]
rs654982	0.87[ASN][1000 genomes]
rs661657	0.85[ASN][1000 genomes]
rs662834	0.87[ASN][1000 genomes]
rs664839	0.87[ASN][1000 genomes]
rs665728	0.89[ASN][1000 genomes]
rs665894	0.85[ASN][1000 genomes]
rs666254	0.89[ASN][1000 genomes]
rs668070	0.81[ASN][1000 genomes]
rs670932	0.87[ASN][1000 genomes]
rs671364	0.87[ASN][1000 genomes]
rs674543	0.83[ASN][1000 genomes]
rs688176	0.86[ASN][1000 genomes]
rs694903	0.84[ASN][1000 genomes]
rs707991	0.82[ASN][1000 genomes]
rs7756630	0.82[ASN][1000 genomes]
rs9378395	0.86[ASN][1000 genomes]
rs9405219	0.86[ASN][1000 genomes]
rs942475	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3444323	chr6:4078453-4080526	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4066800-4079600	Weak transcription	NHLF	lung
2	chr6:4067000-4082400	Weak transcription	Brain Germinal Matrix	brain
3	chr6:4074400-4083000	Weak transcription	Pancreas	Pancrea
4	chr6:4078200-4084600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:4079000-4082400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:4079200-4079800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr6:4079200-4080000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:4079400-4092000	Weak transcription	Right Atrium	heart

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