Variant report

Variant	rs28520677
Chromosome Location	chr6:39290540-39290541
allele	C/T
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:1)
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	chr6:39290526-39290576	HCM	heart:	n/a
2	chr6:39290526-39290576	AG04450	lung:	fetal
3	chr6:39290526-39290576	GM12878	blood:	n/a
4	chr6:39290526-39290576	SAEC	small airway:	n/a
5	chr6:39290526-39290576	SK-N-SH_RA	brain:	n/a
6	chr6:39290526-39290576	GM06990	blood:	n/a
7	chr6:39290526-39290576	ovcar-3	ovarian:	n/a
8	chr6:39290526-39290576	RPTEC	kidney:	n/a
9	chr6:39290526-39290576	PANC-1	pancreas:	n/a
10	chr6:39290526-39290576	HCF	heart:	n/a
11	chr6:39290526-39290576	AG09309	skin:	n/a
12	chr6:39290526-39290576	ProgFib	skin:	n/a
13	chr6:39290526-39290576	HL-60	blood:	n/a
14	chr6:39290526-39290576	MCF-7	breast:	n/a
15	chr6:39290526-39290576	AG09319	gingival:	n/a
16	chr6:39290526-39290576	Hela-S3	cervix:	n/a
17	chr6:39290526-39290576	CMK	blood:	n/a
18	chr6:39290526-39290576	SK-N-MC	brain:	n/a
19	chr6:39290526-39290576	GM12891	blood:	n/a
20	chr6:39290526-39290576	HCPEpiC	choroid plexus:	n/a
21	chr6:39290526-39290576	PFSK-1	brain:	n/a
22	chr6:39290526-39290576	HNPCEpiC	eye:	n/a
23	chr6:39290526-39290576	HRE	kidney:	n/a
24	chr6:39290526-39290576	HMEC	breast:	n/a
25	chr6:39290526-39290576	GM19239	blood:	n/a
26	chr6:39290526-39290576	HEK293	kidney:	embryo
27	chr6:39290526-39290576	AG04449	skin:	fetal
28	chr6:39290526-39290576	HRPEpiC	eye:	n/a
29	chr6:39290526-39290576	NT2-D1	testis:	n/a
30	chr6:39290526-39290576	SKMC	muscle:	n/a
31	chr6:39290526-39290576	HepG2	liver:	n/a
32	chr6:39290526-39290576	SK-N-SH	brain:	n/a
33	chr6:39290526-39290576	IMR90	lung:	fetal
34	chr6:39290526-39290576	HCT-116	colon:	n/a
35	chr6:39290526-39290576	K562	blood:	n/a
36	chr6:39290526-39290576	NH-A	brain:	n/a
37	chr6:39290526-39290576	HEEpiC	esophagus:	n/a
38	chr6:39290526-39290576	LNCaP	prostate:	n/a
39	chr6:39290526-39290576	BJ	skin:	n/a
40	chr6:39290526-39290576	Caco-2	colon:	n/a
41	chr6:39290526-39290576	HUVEC	blood vessel:	n/a
42	chr6:39290526-39290576	AG10803	skin:	n/a
43	chr6:39290526-39290576	HIPEpiC	eye:	n/a
44	chr6:39290526-39290576	Hepatocyte	liver:	n/a
45	chr6:39290526-39290576	GM12892	blood:	n/a
46	chr6:39290526-39290576	PrEC	prostate:	n/a
47	chr6:39290526-39290576	HAEpiC	amniotic membrane:	n/a
48	chr6:39290526-39290576	NHBE	bronchial:	n/a
49	chr6:39290526-39290576	AoSMC	blood vessel:	n/a
50	chr6:39290526-39290576	Jurkat	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39195950..39197614-chr6:39288788..39290950,2	K562	blood:

No data

Variant related genes	Relation type
KCNK16	CpG island
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1109772	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751173	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751627	0.89[AMR][1000 genomes]
rs11751657	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753468	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11755807	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755830	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755884	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756311	0.89[AMR][1000 genomes]
rs11758434	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16891904	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41273126	1.00[AMR][1000 genomes]
rs61750316	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61751240	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv533806	chr6:39270073-39397337	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 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	chr6:39282800-39291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:39283000-39295400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:39283400-39291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:39285600-39307800	Weak transcription	Esophagus	oesophagus
5	chr6:39286400-39290800	Enhancers	Primary hematopoietic stem cells	blood
6	chr6:39287400-39291000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr6:39288600-39298000	Weak transcription	Right Atrium	heart
8	chr6:39290000-39290800	Enhancers	Lung	lung

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