Variant report

Variant	rs7954446
Chromosome Location	chr12:49113738-49113739
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:6)
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	chr12:49113738-49113788	BJ	skin:	n/a
2	chr12:49113738-49113788	HCT-116	colon:	n/a
3	chr12:49113738-49113788	SK-N-SH_RA	brain:	n/a
4	chr12:49113738-49113788	HNPCEpiC	eye:	n/a
5	chr12:49113738-49113788	NB4	blood:	n/a
6	chr12:49113738-49113788	MCF10A-Er-Src	breast:	n/a
7	chr12:49113738-49113788	HUVEC	blood vessel:	n/a
8	chr12:49113738-49113788	ovcar-3	ovarian:	n/a
9	chr12:49113738-49113788	NH-A	brain:	n/a
10	chr12:49113738-49113788	Hepatocyte	liver:	n/a
11	chr12:49113738-49113788	NHBE	bronchial:	n/a
12	chr12:49113738-49113788	Hela-S3	cervix:	n/a
13	chr12:49113738-49113788	PFSK-1	brain:	n/a
14	chr12:49113738-49113788	AG10803	skin:	n/a
15	chr12:49113738-49113788	HRCEpiC	kidney:	n/a
16	chr12:49113738-49113788	K562	blood:	n/a
17	chr12:49113738-49113788	SAEC	small airway:	n/a
18	chr12:49113738-49113788	Caco-2	colon:	n/a
19	chr12:49113738-49113788	SKMC	muscle:	n/a
20	chr12:49113738-49113788	AG04449	skin:	fetal
21	chr12:49113738-49113788	PANC-1	pancreas:	n/a
22	chr12:49113738-49113788	AG09309	skin:	n/a
23	chr12:49113738-49113788	HMEC	breast:	n/a
24	chr12:49113738-49113788	GM06990	blood:	n/a
25	chr12:49113738-49113788	GM12892	blood:	n/a
26	chr12:49113738-49113788	HCPEpiC	choroid plexus:	n/a
27	chr12:49113738-49113788	HCM	heart:	n/a
28	chr12:49113738-49113788	HEK293	kidney:	embryo
29	chr12:49113738-49113788	LNCaP	prostate:	n/a
30	chr12:49113738-49113788	PrEC	prostate:	n/a
31	chr12:49113738-49113788	HRE	kidney:	n/a
32	chr12:49113738-49113788	GM19239	blood:	n/a
33	chr12:49113738-49113788	HRPEpiC	eye:	n/a
34	chr12:49113738-49113788	HCF	heart:	n/a
35	chr12:49113738-49113788	RPTEC	kidney:	n/a
36	chr12:49113738-49113788	HEEpiC	esophagus:	n/a
37	chr12:49113738-49113788	SK-N-MC	brain:	n/a
38	chr12:49113738-49113788	AG09319	gingival:	n/a
39	chr12:49113738-49113788	AG04450	lung:	fetal
40	chr12:49113738-49113788	GM12878	blood:	n/a
41	chr12:49113738-49113788	IMR90	lung:	fetal
42	chr12:49113738-49113788	H1-hESC	embryonic stem cell:	embryo
43	chr12:49113738-49113788	SK-N-SH	brain:	n/a
44	chr12:49113738-49113788	ProgFib	skin:	n/a
45	chr12:49113738-49113788	CMK	blood:	n/a
46	chr12:49113738-49113788	HAEpiC	amniotic membrane:	n/a
47	chr12:49113738-49113788	NHDF-neo	bronchial:	n/a
48	chr12:49113738-49113788	MCF-7	breast:	n/a
49	chr12:49113738-49113788	U87	brain:	n/a
50	chr12:49113738-49113788	HPAEpiC	pulmonary alveolar:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49110692..49113146-chr12:49113655..49115312,2	K562	blood:
2	chr12:49112523..49114853-chr12:49207159..49208683,2	MCF-7	breast:
3	chr12:49111500..49113785-chr12:49114304..49115934,2	MCF-7	breast:
4	chr12:49108509..49113146-chr12:49113655..49117535,6	K562	blood:
5	chr12:49112410..49114208-chr12:49118844..49121156,2	K562	blood:
6	chr12:49111079..49113918-chr12:49181891..49183549,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCNT1	CpG island
ENSG00000174233	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000257660	Chromatin interaction
ENSG00000129315	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10747554	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10783273	0.80[ASN][1000 genomes]
rs10783275	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783278	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783281	0.94[EUR][1000 genomes]
rs10875850	0.81[ASN][1000 genomes]
rs10875852	0.86[ASN][1000 genomes]
rs10875853	0.86[ASN][1000 genomes]
rs10875861	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875862	0.94[ASN][1000 genomes]
rs10875869	0.81[EUR][1000 genomes]
rs10875870	0.83[EUR][1000 genomes]
rs10875871	0.82[EUR][1000 genomes]
rs1110432	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168657	0.81[ASN][1000 genomes]
rs11168665	0.86[ASN][1000 genomes]
rs11168674	0.83[ASN][1000 genomes]
rs11168697	0.89[ASN][1000 genomes]
rs11168698	0.95[ASN][1000 genomes]
rs12426435	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1316514	0.95[ASN][1000 genomes]
rs1863541	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1895995	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2114320	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2162317	0.93[ASN][1000 genomes]
rs2277365	0.87[ASN][1000 genomes]
rs2277366	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2291728	0.95[ASN][1000 genomes]
rs2409085	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2898087	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3209584	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35717253	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3741628	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3741629	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3741630	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741632	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3803025	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3943899	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4113946	0.81[ASN][1000 genomes]
rs4500528	0.86[ASN][1000 genomes]
rs4760735	0.81[ASN][1000 genomes]
rs4760737	0.82[ASN][1000 genomes]
rs4760739	0.80[ASN][1000 genomes]
rs4760740	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6580689	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6580690	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580693	0.98[EUR][1000 genomes]
rs7138190	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138930	0.81[EUR][1000 genomes]
rs7139236	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7299276	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304711	0.81[ASN][1000 genomes]
rs7305907	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306604	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7308699	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314665	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7964546	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966065	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7974625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975030	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332441	0.85[ASN][1000 genomes]
rs9634241	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9634242	0.86[ASN][1000 genomes]
rs9634262	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7954446	WNT10B	cis	Muscle Skeletal	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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