Variant report

Variant	rs608841
Chromosome Location	chr3:138764229-138764230
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	chr3:138764193-138764243	GM12891	blood:	n/a
2	chr3:138764193-138764243	PFSK-1	brain:	n/a
3	chr3:138764193-138764243	Jurkat	blood:	n/a
4	chr3:138764193-138764243	H1-hESC	embryonic stem cell:	embryo
5	chr3:138764193-138764243	CMK	blood:	n/a
6	chr3:138764193-138764243	GM06990	blood:	n/a
7	chr3:138764193-138764243	HEEpiC	esophagus:	n/a
8	chr3:138764193-138764243	NH-A	brain:	n/a
9	chr3:138764193-138764243	HRE	kidney:	n/a
10	chr3:138764193-138764243	LNCaP	prostate:	n/a
11	chr3:138764193-138764243	ovcar-3	ovarian:	n/a
12	chr3:138764193-138764243	SAEC	small airway:	n/a
13	chr3:138764193-138764243	AG04450	lung:	fetal
14	chr3:138764193-138764243	HEK293	kidney:	embryo
15	chr3:138764193-138764243	AoSMC	blood vessel:	n/a
16	chr3:138764193-138764243	T-47D	breast:	n/a
17	chr3:138764193-138764243	BJ	skin:	n/a
18	chr3:138764193-138764243	AG09309	skin:	n/a
19	chr3:138764193-138764243	NHBE	bronchial:	n/a
20	chr3:138764193-138764243	AG04449	skin:	fetal
21	chr3:138764193-138764243	HPAEpiC	pulmonary alveolar:	n/a
22	chr3:138764193-138764243	IMR90	lung:	fetal
23	chr3:138764193-138764243	SK-N-SH	brain:	n/a
24	chr3:138764193-138764243	NHDF-neo	bronchial:	n/a
25	chr3:138764193-138764243	A549	lung:	n/a
26	chr3:138764193-138764243	SK-N-MC	brain:	n/a
27	chr3:138764193-138764243	PANC-1	pancreas:	n/a
28	chr3:138764193-138764243	MCF10A-Er-Src	breast:	n/a
29	chr3:138764193-138764243	PrEC	prostate:	n/a
30	chr3:138764193-138764243	Caco-2	colon:	n/a
31	chr3:138764193-138764243	Hela-S3	cervix:	n/a
32	chr3:138764193-138764243	SKMC	muscle:	n/a
33	chr3:138764193-138764243	NB4	blood:	n/a
34	chr3:138764193-138764243	MCF-7	breast:	n/a
35	chr3:138764193-138764243	HIPEpiC	eye:	n/a
36	chr3:138764193-138764243	RPTEC	kidney:	n/a
37	chr3:138764193-138764243	HNPCEpiC	eye:	n/a
38	chr3:138764193-138764243	HCT-116	colon:	n/a
39	chr3:138764193-138764243	BE2_C	brain:	n/a
40	chr3:138764193-138764243	ECC-1	luminal epithelium:	n/a
41	chr3:138764193-138764243	HL-60	blood:	n/a
42	chr3:138764193-138764243	HRPEpiC	eye:	n/a
43	chr3:138764193-138764243	GM19239	blood:	n/a
44	chr3:138764193-138764243	NT2-D1	testis:	n/a
45	chr3:138764193-138764243	HepG2	liver:	n/a
46	chr3:138764193-138764243	K562	blood:	n/a
47	chr3:138764193-138764243	U87	brain:	n/a
48	chr3:138764193-138764243	AG09319	gingival:	n/a
49	chr3:138764193-138764243	GM12878	blood:	n/a
50	chr3:138764193-138764243	AG10803	skin:	n/a

No data

Variant related genes	Relation type
PRR23C	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10935297	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11919100	0.87[EUR][1000 genomes]
rs11924188	0.89[EUR][1000 genomes]
rs1521557	0.84[CHB][hapmap]
rs1851265	0.94[EUR][1000 genomes]
rs2246671	0.81[CHB][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs2667303	0.81[MEX][hapmap];0.85[TSI][hapmap]
rs360702	0.85[EUR][1000 genomes]
rs360703	0.85[EUR][1000 genomes]
rs360704	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4894335	0.83[EUR][1000 genomes]
rs607573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661711	1.00[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs885257	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv829736	chr3:138737352-138934758	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138757400-138765200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:138764200-138766000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links