Variant report

Variant	rs2568047
Chromosome Location	chr11:9010006-9010007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr11:9009860-9010501	K562	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9010332-9010339 chr11:9010332-9010339
2	JUN	chr11:9009950-9010572	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
3	GABPA	chr11:9009871-9010522	K562	blood:	n/a	n/a
4	POLR2A	chr11:9009834-9010605	K562	blood:	n/a	n/a
5	HMGN3	chr11:9009856-9010491	K562	blood:	n/a	chr11:9010387-9010396
6	MYC	chr11:9009854-9010526	K562	blood:	n/a	n/a
7	GATA2	chr11:9009787-9010646	K562	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9009840-9009851 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
8	SMARCB1	chr11:9009830-9010745	K562	blood:	n/a	chr11:9010386-9010395
9	BHLHE40	chr11:9009989-9010608	K562	blood:	n/a	n/a
10	RCOR1	chr11:9009812-9010638	K562	blood:	n/a	n/a
11	IRF1	chr11:9009884-9010619	K562	blood:	n/a	n/a
12	GATA2	chr11:9009859-9010566	K562	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
13	STAT5A	chr11:9009786-9010635	K562	blood:	n/a	n/a
14	EP300	chr11:9009861-9010612	K562	blood:	n/a	n/a
15	TBL1XR1	chr11:9009946-9010610	K562	blood:	n/a	n/a
16	TEAD4	chr11:9009771-9011748	K562	blood:	n/a	n/a
17	PML	chr11:9009843-9010607	K562	blood:	n/a	n/a
18	PML	chr11:9009771-9010635	K562	blood:	n/a	n/a
19	CEBPB	chr11:9009845-9010496	K562	blood:	n/a	n/a
20	MAZ	chr11:9009992-9010557	K562	blood:	n/a	n/a
21	HDAC2	chr11:9009829-9010595	K562	blood:	n/a	chr11:9010141-9010155
22	CCNT2	chr11:9009733-9010551	K562	blood:	n/a	chr11:9010330-9010350
23	TEAD4	chr11:9009765-9010691	K562	blood:	n/a	n/a
24	NFYA	chr11:9009913-9010461	K562	blood:	n/a	n/a
25	POLR2A	chr11:9009750-9010654	K562	blood:	n/a	n/a
26	NR2F2	chr11:9009827-9010569	K562	blood:	n/a	n/a
27	TRIM28	chr11:9009773-9010679	K562	blood:	n/a	n/a
28	STAT5A	chr11:9009803-9010599	K562	blood:	n/a	n/a
29	CBX3	chr11:9009915-9010632	K562	blood:	n/a	n/a
30	POLR2A	chr11:9009863-9010539	K562	blood:	n/a	n/a
31	MAFF	chr11:9009908-9010598	K562	blood:	n/a	n/a
32	CUX1	chr11:9009950-9010106	K562	blood:	n/a	n/a
33	REST	chr11:9009878-9010144	K562	blood:	n/a	n/a
34	EP300	chr11:9009931-9010512	K562	blood:	n/a	n/a
35	JUN	chr11:9009512-9011924	K562	blood:	n/a	chr11:9010385-9010395 chr11:9011084-9011092 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9011083-9011093 chr11:9010385-9010395 chr11:9011200-9011209 chr11:9011085-9011096 chr11:9011084-9011091
36	MXI1	chr11:9010005-9010449	K562	blood:	n/a	n/a
37	UBTF	chr11:9009886-9010746	K562	blood:	n/a	n/a
38	NR2F2	chr11:9009737-9010726	K562	blood:	n/a	n/a
39	CEBPD	chr11:9009805-9010653	K562	blood:	n/a	n/a
40	ZMIZ1	chr11:9009880-9010537	K562	blood:	n/a	n/a
41	JUND	chr11:9009881-9010637	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
42	ATF1	chr11:9009912-9010556	K562	blood:	n/a	n/a
43	MYC	chr11:9009949-9010614	K562	blood:	n/a	n/a
44	JUN	chr11:9010001-9010579	K562	blood:	n/a	chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010385-9010395 chr11:9010386-9010394 chr11:9010385-9010395
45	POLR2A	chr11:9009857-9010575	K562	blood:	n/a	n/a
46	CEBPD	chr11:9009801-9010656	K562	blood:	n/a	n/a
47	GATA1	chr11:9009690-9010922	PBDE	blood:	n/a	chr11:9010331-9010341 chr11:9010333-9010350 chr11:9010533-9010546 chr11:9010332-9010339 chr11:9010332-9010341 chr11:9010384-9010393 chr11:9010325-9010346 chr11:9009840-9009851 chr11:9010332-9010339 chr11:9010535-9010543 chr11:9010332-9010339
48	TAL1	chr11:9009672-9010658	K562	blood:	n/a	chr11:9010332-9010350 chr11:9010331-9010339
49	ARID3A	chr11:9009838-9010684	K562	blood:	n/a	chr11:9010619-9010635
50	RCOR1	chr11:9009882-9010597	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:8985934..8987677-chr11:9008454..9010200,2	K562	blood:
2	chr11:8992487..8994704-chr11:9009691..9012434,3	K562	blood:
3	chr11:8981281..8983336-chr11:9009757..9012558,2	K562	blood:
4	chr11:9008310..9013368-chr11:9022083..9026889,11	K562	blood:

Variant related genes	Relation type
NRIP3	TF binding region
ENSG00000254860	Chromatin interaction
ENSG00000253973	Chromatin interaction
ENSG00000175352	Chromatin interaction
ENSG00000175348	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10219366	0.81[EUR][1000 genomes]
rs1025438	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs10769974	0.82[GIH][hapmap]
rs10769976	0.83[EUR][1000 genomes]
rs10840151	0.82[GIH][hapmap]
rs10840156	0.83[EUR][1000 genomes]
rs1133833	0.81[MEX][hapmap]
rs1136966	0.95[MEX][hapmap]
rs12785559	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12786377	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790020	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12798311	0.80[EUR][1000 genomes]
rs12805109	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347016	0.87[ASN][1000 genomes]
rs1960180	0.84[CHD][hapmap]
rs1984775	0.80[CEU][hapmap]
rs1985026	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016844	0.84[CHD][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2056903	0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2116510	0.84[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs2116511	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2163625	0.82[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs2246878	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2247038	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2252102	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316541	0.85[ASN][1000 genomes]
rs2568029	0.86[MEX][hapmap]
rs2568069	0.84[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2568074	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568075	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568077	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2568079	0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568081	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2568086	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568087	0.87[ASN][1000 genomes]
rs2568088	0.81[ASN][1000 genomes]
rs2653565	0.81[MEX][hapmap];0.81[TSI][hapmap]
rs2653590	0.87[ASN][1000 genomes]
rs2653601	0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2653604	0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs2653611	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742473	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742486	0.87[ASN][1000 genomes]
rs2742487	0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2742488	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2742489	0.81[ASN][1000 genomes]
rs2742491	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2742493	0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs2742495	0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742496	0.84[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2742497	0.91[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742502	0.86[MEX][hapmap]
rs2742504	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742505	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742512	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742513	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742514	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2742519	0.84[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs3751058	0.84[CHD][hapmap]
rs3751063	0.80[GIH][hapmap];0.83[EUR][1000 genomes]
rs3751068	0.82[GIH][hapmap];0.81[MEX][hapmap]
rs3763912	0.82[GIH][hapmap]
rs3829273	0.81[CHD][hapmap]
rs4061640	0.80[CEU][hapmap]
rs4264185	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4370967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4909951	0.82[GIH][hapmap];0.83[EUR][1000 genomes]
rs4910068	0.86[MEX][hapmap]
rs4910313	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486061	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs66630602	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7124403	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125458	0.91[MEX][hapmap]
rs72852790	0.85[ASN][1000 genomes]
rs72853712	0.85[ASN][1000 genomes]
rs7936201	0.80[CEU][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap]
rs7940895	0.87[ASN][1000 genomes]
rs7941341	0.82[MEX][hapmap]
rs909464	0.81[EUR][1000 genomes]
rs9300096	0.82[GIH][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2568047	PRKCDBP	cis	parietal	SCAN
rs2568047	C11orf17	cis	multi-tissue	Pritchard
rs2568047	EIF3F	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8987000-9010200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:8987000-9011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:8987800-9010200	Weak transcription	NHDF-Ad	bronchial
4	chr11:8987800-9012000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr11:8989600-9011200	Weak transcription	Brain Anterior Caudate	brain
6	chr11:8989600-9019600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:8991800-9015600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:9001800-9015200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:9005600-9010200	Weak transcription	HUVEC	blood vessel
10	chr11:9005600-9010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:9008800-9010200	Weak transcription	Aorta	Aorta
12	chr11:9009600-9010800	Flanking Active TSS	K562	blood
13	chr11:9009600-9011600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr11:9009800-9011800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:9010000-9011000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:9010000-9011200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:9010000-9011200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:9010000-9011600	Enhancers	Hela-S3	cervix
19	chr11:9010000-9011600	Enhancers	HSMM	muscle
20	chr11:9010000-9011800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:9010000-9011800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:9010000-9012000	Enhancers	NHLF	lung

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