Variant report

Variant	rs11168435
Chromosome Location	chr12:48562988-48562989
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
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	POLR2A	chr12:48562973-48563312	Gliobla	brain:	n/a	n/a
2	POLR2A	chr12:48562975-48562991	A549	lung:	n/a	n/a
3	POLR2A	chr12:48562978-48563003	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48562943-48562993	GM19239	blood:	n/a
2	chr12:48562943-48562993	HCPEpiC	choroid plexus:	n/a
3	chr12:48562943-48562993	LNCaP	prostate:	n/a
4	chr12:48562943-48562993	BJ	skin:	n/a
5	chr12:48562943-48562993	AoSMC	blood vessel:	n/a
6	chr12:48562943-48562993	GM12891	blood:	n/a
7	chr12:48562943-48562993	PANC-1	pancreas:	n/a
8	chr12:48562943-48562993	GM06990	blood:	n/a
9	chr12:48562943-48562993	NHBE	bronchial:	n/a
10	chr12:48562943-48562993	RPTEC	kidney:	n/a
11	chr12:48562943-48562993	HCT-116	colon:	n/a
12	chr12:48562943-48562993	AG10803	skin:	n/a
13	chr12:48562943-48562993	AG04450	lung:	fetal
14	chr12:48562943-48562993	HepG2	liver:	n/a
15	chr12:48562943-48562993	SK-N-MC	brain:	n/a
16	chr12:48562943-48562993	SK-N-SH	brain:	n/a
17	chr12:48562943-48562993	HUVEC	blood vessel:	n/a
18	chr12:48562943-48562993	GM12878	blood:	n/a
19	chr12:48562943-48562993	NHDF-neo	bronchial:	n/a
20	chr12:48562943-48562993	PFSK-1	brain:	n/a
21	chr12:48562943-48562993	ECC-1	luminal epithelium:	n/a
22	chr12:48562943-48562993	T-47D	breast:	n/a
23	chr12:48562943-48562993	ProgFib	skin:	n/a
24	chr12:48562943-48562993	AG04449	skin:	fetal
25	chr12:48562943-48562993	Caco-2	colon:	n/a
26	chr12:48562943-48562993	Hela-S3	cervix:	n/a
27	chr12:48562943-48562993	NB4	blood:	n/a
28	chr12:48562943-48562993	HNPCEpiC	eye:	n/a
29	chr12:48562943-48562993	HCM	heart:	n/a
30	chr12:48562943-48562993	NT2-D1	testis:	n/a
31	chr12:48562943-48562993	HIPEpiC	eye:	n/a
32	chr12:48562943-48562993	MCF10A-Er-Src	breast:	n/a
33	chr12:48562943-48562993	H1-hESC	embryonic stem cell:	embryo
34	chr12:48562943-48562993	NH-A	brain:	n/a
35	chr12:48562943-48562993	GM12892	blood:	n/a
36	chr12:48562943-48562993	HRE	kidney:	n/a
37	chr12:48562943-48562993	Hepatocyte	liver:	n/a
38	chr12:48562943-48562993	HEEpiC	esophagus:	n/a
39	chr12:48562943-48562993	HMEC	breast:	n/a
40	chr12:48562943-48562993	HRPEpiC	eye:	n/a
41	chr12:48562943-48562993	BE2_C	brain:	n/a
42	chr12:48562943-48562993	Jurkat	blood:	n/a
43	chr12:48562943-48562993	AG09319	gingival:	n/a
44	chr12:48562943-48562993	K562	blood:	n/a
45	chr12:48562943-48562993	CMK	blood:	n/a
46	chr12:48562943-48562993	A549	lung:	n/a
47	chr12:48562943-48562993	IMR90	lung:	fetal
48	chr12:48562943-48562993	PrEC	prostate:	n/a
49	chr12:48562943-48562993	HAEpiC	amniotic membrane:	n/a
50	chr12:48562943-48562993	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr12:48549682..48552268-chr12:48561692..48563746,2	K562	blood:
2	chr12:48551148..48552785-chr12:48562414..48564360,2	MCF-7	breast:
3	chr12:48515800..48518794-chr12:48562400..48565355,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257848	TF binding region
ENSG00000257848	CpG island
ENSG00000152556	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1049392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10747529	1.00[JPT][hapmap]
rs10783235	0.89[MEX][hapmap];0.90[MKK][hapmap]
rs10875733	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs10875739	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10875752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875754	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10875759	0.85[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875761	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];0.95[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875765	0.89[ASN][1000 genomes]
rs10875766	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168350	0.94[JPT][hapmap]
rs11168353	0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168363	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168364	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168373	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11168378	0.83[EUR][1000 genomes]
rs11168404	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs11168412	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11168417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs11168419	0.82[ASN][1000 genomes]
rs11168424	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168438	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11168439	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11168442	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168443	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11168444	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168445	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168446	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168448	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168453	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11168454	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11834818	0.84[EUR][1000 genomes]
rs12228924	0.90[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12422355	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12425679	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12426981	0.86[EUR][1000 genomes]
rs17122567	0.88[GIH][hapmap];1.00[JPT][hapmap]
rs1859443	0.94[JPT][hapmap]
rs1978161	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2171643	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2286020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2408954	1.00[JPT][hapmap]
rs3742075	0.88[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs3825403	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs4258439	1.00[JPT][hapmap]
rs56097189	0.93[ASN][1000 genomes]
rs57430775	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58540891	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58556309	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59537300	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580658	0.88[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs66507954	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7132898	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133274	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7136243	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7136782	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7136788	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299704	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7302354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7303677	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73104071	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73105950	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73304926	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7484942	1.00[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs765260	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7962390	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7962569	1.00[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8181670	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];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs886589	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs954326	0.94[JPT][hapmap]
rs9651981	0.91[GIH][hapmap];0.94[JPT][hapmap]
rs9804751	0.92[GIH][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv976608	chr12:48558446-48563571	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168435	TMEM106C	cis	parietal	SCAN
rs11168435	C12orf41	cis	parietal	SCAN
rs11168435	ZNF641	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48562600-48563000	Bivalent/Poised TSS	HepG2	liver
2	chr12:48562600-48563200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links