Variant report

Variant	rs2296837
Chromosome Location	chr1:166958601-166958602
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
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	E2F6	chr1:166958159-166958874	H1-hESC	embryonic stem cell:	n/a	chr1:166958496-166958505 chr1:166958469-166958478 chr1:166958337-166958346
2	E2F6	chr1:166958303-166958889	H1-hESC	embryonic stem cell:	n/a	chr1:166958496-166958505 chr1:166958469-166958478 chr1:166958337-166958346
3	POLR2A	chr1:166958580-166958842	MCF-7	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:166958583-166958633	ProgFib	skin:	n/a
2	chr1:166958581-166958631	Jurkat	blood:	n/a
3	chr1:166958581-166958631	HepG2	liver:	n/a
4	chr1:166958581-166958631	Hela-S3	cervix:	n/a
5	chr1:166958583-166958633	Hepatocyte	liver:	n/a
6	chr1:166958583-166958633	H1-hESC	embryonic stem cell:	embryo
7	chr1:166958581-166958631	NH-A	brain:	n/a
8	chr1:166958581-166958631	SAEC	small airway:	n/a
9	chr1:166958581-166958631	NHBE	bronchial:	n/a
10	chr1:166958581-166958631	HCF	heart:	n/a
11	chr1:166958581-166958631	HL-60	blood:	n/a
12	chr1:166958581-166958631	PFSK-1	brain:	n/a
13	chr1:166958583-166958633	U87	brain:	n/a
14	chr1:166958583-166958633	HCM	heart:	n/a
15	chr1:166958583-166958633	NT2-D1	testis:	n/a
16	chr1:166958583-166958633	HPAEpiC	pulmonary alveolar:	n/a
17	chr1:166958581-166958631	SK-N-MC	brain:	n/a
18	chr1:166958583-166958633	HCPEpiC	choroid plexus:	n/a
19	chr1:166958583-166958633	AG09309	skin:	n/a
20	chr1:166958583-166958633	GM06990	blood:	n/a
21	chr1:166958581-166958631	MCF-7	breast:	n/a
22	chr1:166958583-166958633	MCF-7	breast:	n/a
23	chr1:166958583-166958633	BE2_C	brain:	n/a
24	chr1:166958583-166958633	SK-N-SH	brain:	n/a
25	chr1:166958581-166958631	K562	blood:	n/a
26	chr1:166958583-166958633	ovcar-3	ovarian:	n/a
27	chr1:166958581-166958631	PANC-1	pancreas:	n/a
28	chr1:166958581-166958631	Hepatocyte	liver:	n/a
29	chr1:166958583-166958633	HAEpiC	amniotic membrane:	n/a
30	chr1:166958583-166958633	GM12878	blood:	n/a
31	chr1:166958583-166958633	SK-N-MC	brain:	n/a
32	chr1:166958581-166958631	HRCEpiC	kidney:	n/a
33	chr1:166958581-166958631	LNCaP	prostate:	n/a
34	chr1:166958583-166958633	SKMC	muscle:	n/a
35	chr1:166958583-166958633	AG10803	skin:	n/a
36	chr1:166958581-166958631	HCM	heart:	n/a
37	chr1:166958581-166958631	AG04450	lung:	fetal
38	chr1:166958581-166958631	AG04449	skin:	fetal
39	chr1:166958583-166958633	HUVEC	blood vessel:	n/a
40	chr1:166958581-166958631	BE2_C	brain:	n/a
41	chr1:166958583-166958633	HNPCEpiC	eye:	n/a
42	chr1:166958583-166958633	SAEC	small airway:	n/a
43	chr1:166958581-166958631	AG09309	skin:	n/a
44	chr1:166958583-166958633	NHBE	bronchial:	n/a
45	chr1:166958583-166958633	HepG2	liver:	n/a
46	chr1:166958581-166958631	HRPEpiC	eye:	n/a
47	chr1:166958583-166958633	SK-N-SH_RA	brain:	n/a
48	chr1:166958581-166958631	NT2-D1	testis:	n/a
49	chr1:166958583-166958633	AG04449	skin:	fetal
50	chr1:166958581-166958631	ECC-1	luminal epithelium:	n/a

No data

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

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1041238	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10918607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10918608	0.86[ASN][1000 genomes]
rs11578336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11802666	0.87[ASN][1000 genomes]
rs11805946	0.88[ASN][1000 genomes]
rs12118335	0.81[ASN][1000 genomes]
rs12126991	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12131832	0.85[ASN][1000 genomes]
rs12133327	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12134016	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12564877	0.86[ASN][1000 genomes]
rs12569084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2312487	0.86[ASN][1000 genomes]
rs2312675	0.80[CHB][hapmap]
rs3736988	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs41269702	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56093705	0.81[ASN][1000 genomes]
rs61447801	0.88[ASN][1000 genomes]
rs61606407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427053	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs6655947	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6660048	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6662130	0.88[ASN][1000 genomes]
rs6665341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669886	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6673622	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6673720	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6681562	0.85[ASN][1000 genomes]
rs6681571	0.84[ASN][1000 genomes]
rs6682062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6695609	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6696203	0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6697417	0.90[ASN][1000 genomes]
rs6699159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7511933	0.88[ASN][1000 genomes]
rs7518155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7533688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7545911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004148	chr1:166951869-167016311	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2750815	chr1:166953866-167180342	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166958400-166958800	Active TSS	Spleen	Spleen
2	chr1:166958400-166959000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:166958400-166964600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:166958600-166959200	Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links