Variant report

Variant	rs3753868
Chromosome Location	chr1:159557269-159557270
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	chr1:159557257-159557307	HL-60	blood:	n/a
2	chr1:159557257-159557307	SK-N-SH	brain:	n/a
3	chr1:159557257-159557307	BJ	skin:	n/a
4	chr1:159557257-159557307	GM12891	blood:	n/a
5	chr1:159557257-159557307	HEK293	kidney:	embryo
6	chr1:159557257-159557307	PANC-1	pancreas:	n/a
7	chr1:159557257-159557307	NT2-D1	testis:	n/a
8	chr1:159557257-159557307	HNPCEpiC	eye:	n/a
9	chr1:159557257-159557307	AG04450	lung:	fetal
10	chr1:159557257-159557307	Hepatocyte	liver:	n/a
11	chr1:159557257-159557307	HCF	heart:	n/a
12	chr1:159557257-159557307	GM12892	blood:	n/a
13	chr1:159557257-159557307	HRE	kidney:	n/a
14	chr1:159557257-159557307	MCF-7	breast:	n/a
15	chr1:159557257-159557307	SK-N-SH_RA	brain:	n/a
16	chr1:159557257-159557307	IMR90	lung:	fetal
17	chr1:159557257-159557307	HRPEpiC	eye:	n/a
18	chr1:159557257-159557307	AoSMC	blood vessel:	n/a
19	chr1:159557257-159557307	HCM	heart:	n/a
20	chr1:159557257-159557307	NHBE	bronchial:	n/a
21	chr1:159557257-159557307	RPTEC	kidney:	n/a
22	chr1:159557257-159557307	U87	brain:	n/a
23	chr1:159557257-159557307	GM12878	blood:	n/a
24	chr1:159557257-159557307	ProgFib	skin:	n/a
25	chr1:159557257-159557307	ECC-1	luminal epithelium:	n/a
26	chr1:159557257-159557307	HepG2	liver:	n/a
27	chr1:159557257-159557307	NHDF-neo	bronchial:	n/a
28	chr1:159557257-159557307	AG10803	skin:	n/a
29	chr1:159557257-159557307	MCF10A-Er-Src	breast:	n/a
30	chr1:159557257-159557307	PrEC	prostate:	n/a
31	chr1:159557257-159557307	Jurkat	blood:	n/a
32	chr1:159557257-159557307	HEEpiC	esophagus:	n/a
33	chr1:159557257-159557307	HUVEC	blood vessel:	n/a
34	chr1:159557257-159557307	HCPEpiC	choroid plexus:	n/a
35	chr1:159557257-159557307	SK-N-MC	brain:	n/a
36	chr1:159557257-159557307	NH-A	brain:	n/a
37	chr1:159557257-159557307	CMK	blood:	n/a
38	chr1:159557257-159557307	Hela-S3	cervix:	n/a
39	chr1:159557257-159557307	K562	blood:	n/a
40	chr1:159557257-159557307	AG04449	skin:	fetal
41	chr1:159557257-159557307	H1-hESC	embryonic stem cell:	embryo
42	chr1:159557257-159557307	PFSK-1	brain:	n/a
43	chr1:159557257-159557307	NB4	blood:	n/a
44	chr1:159557257-159557307	AG09319	gingival:	n/a
45	chr1:159557257-159557307	BE2_C	brain:	n/a
46	chr1:159557257-159557307	A549	lung:	n/a
47	chr1:159557257-159557307	AG09309	skin:	n/a
48	chr1:159557257-159557307	HCT-116	colon:	n/a
49	chr1:159557257-159557307	GM19239	blood:	n/a
50	chr1:159557257-159557307	HIPEpiC	eye:	n/a

No data

Variant related genes	Relation type
APCS	CpG island
OR10AE1P	CpG island

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1037143	0.87[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap]
rs1037144	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs1037145	0.87[CHD][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap]
rs10494329	0.92[JPT][hapmap]
rs10797050	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908736	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908737	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265240	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156411	0.95[ASN][1000 genomes]
rs11804578	0.92[JPT][hapmap]
rs12037510	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1374486	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446966	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs1562384	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17457476	0.92[JPT][hapmap]
rs1900393	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955160	0.92[JPT][hapmap]
rs2197619	0.95[ASN][1000 genomes]
rs2244698	0.96[ASN][1000 genomes]
rs2794523	1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs2794524	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs3753867	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4584389	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61582984	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681315	0.90[ASN][1000 genomes]
rs6689429	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695377	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6695494	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7527322	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7530926	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7531040	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7541411	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3753868	APCS	cis	cerebellum	SCAN
rs3753868	F11R	cis	parietal	SCAN
rs3753868	AIM2	cis	parietal	SCAN
rs3753868	MUC1	cis	parietal	SCAN
rs3753868	APCS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159556800-159557400	Flanking Active TSS	Liver	Liver
2	chr1:159557200-159557800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links