Variant report

Variant	rs11969981
Chromosome Location	chr6:25650817-25650818
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:25650538-25650823	SH-SY5Y	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:25650786-25650836	HepG2	liver:	n/a
2	chr6:25650786-25650836	AG09309	skin:	n/a
3	chr6:25650786-25650836	HAEpiC	amniotic membrane:	n/a
4	chr6:25650786-25650836	HUVEC	blood vessel:	n/a
5	chr6:25650786-25650836	RPTEC	kidney:	n/a
6	chr6:25650786-25650836	HRPEpiC	eye:	n/a
7	chr6:25650786-25650836	SK-N-MC	brain:	n/a
8	chr6:25650786-25650836	HNPCEpiC	eye:	n/a
9	chr6:25650786-25650836	NH-A	brain:	n/a
10	chr6:25650786-25650836	T-47D	breast:	n/a
11	chr6:25650786-25650836	PrEC	prostate:	n/a
12	chr6:25650786-25650836	AG10803	skin:	n/a
13	chr6:25650786-25650836	SK-N-SH_RA	brain:	n/a
14	chr6:25650786-25650836	HCM	heart:	n/a
15	chr6:25650786-25650836	NT2-D1	testis:	n/a
16	chr6:25650786-25650836	HCF	heart:	n/a
17	chr6:25650786-25650836	SAEC	small airway:	n/a
18	chr6:25650786-25650836	GM12878	blood:	n/a
19	chr6:25650786-25650836	IMR90	lung:	fetal
20	chr6:25650786-25650836	BJ	skin:	n/a
21	chr6:25650786-25650836	Hela-S3	cervix:	n/a
22	chr6:25650786-25650836	Hepatocyte	liver:	n/a
23	chr6:25650786-25650836	A549	lung:	n/a
24	chr6:25650786-25650836	HRCEpiC	kidney:	n/a
25	chr6:25650786-25650836	GM06990	blood:	n/a
26	chr6:25650786-25650836	HEEpiC	esophagus:	n/a
27	chr6:25650786-25650836	AG04450	lung:	fetal
28	chr6:25650786-25650836	GM12892	blood:	n/a
29	chr6:25650786-25650836	NB4	blood:	n/a
30	chr6:25650786-25650836	AG04449	skin:	fetal
31	chr6:25650786-25650836	MCF10A-Er-Src	breast:	n/a
32	chr6:25650786-25650836	LNCaP	prostate:	n/a
33	chr6:25650786-25650836	GM19239	blood:	n/a
34	chr6:25650786-25650836	K562	blood:	n/a
35	chr6:25650786-25650836	AG09319	gingival:	n/a
36	chr6:25650786-25650836	GM12891	blood:	n/a
37	chr6:25650786-25650836	HL-60	blood:	n/a
38	chr6:25650786-25650836	ECC-1	luminal epithelium:	n/a
39	chr6:25650786-25650836	Caco-2	colon:	n/a
40	chr6:25650786-25650836	HCT-116	colon:	n/a
41	chr6:25650786-25650836	SKMC	muscle:	n/a
42	chr6:25650786-25650836	ProgFib	skin:	n/a
43	chr6:25650786-25650836	H1-hESC	embryonic stem cell:	embryo
44	chr6:25650786-25650836	ovcar-3	ovarian:	n/a
45	chr6:25650786-25650836	U87	brain:	n/a
46	chr6:25650786-25650836	HCPEpiC	choroid plexus:	n/a
47	chr6:25650786-25650836	PFSK-1	brain:	n/a
48	chr6:25650786-25650836	HRE	kidney:	n/a
49	chr6:25650786-25650836	CMK	blood:	n/a
50	chr6:25650786-25650836	HIPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25639036..25640680-chr6:25649432..25650985,2	K562	blood:

No data

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1028319	1.00[AFR][1000 genomes]
rs10498728	1.00[YRI][hapmap]
rs12526321	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12528159	1.00[AFR][1000 genomes]
rs17252870	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17253044	1.00[JPT][hapmap]
rs17322552	1.00[YRI][hapmap]
rs17491869	1.00[AFR][1000 genomes]
rs2064128	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs214055	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2294344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs301393	1.00[JPT][hapmap]
rs35676593	1.00[AFR][1000 genomes]
rs3788994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3804133	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3923725	1.00[YRI][hapmap]
rs4140641	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419666	1.00[YRI][hapmap]
rs4712950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57141743	1.00[AFR][1000 genomes]
rs60626645	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61340952	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
4	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25641200-25651800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:25643800-25651400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:25649000-25652000	Enhancers	Brain Germinal Matrix	brain

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