Variant report

Variant	rs11812048
Chromosome Location	chr1:227511074-227511075
allele	C/T
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	chr1:227511044-227511549	SH-SY5Y	brain:	n/a	n/a
2	CHD2	chr1:227510934-227511850	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr1:227510989-227511768	MCF-7	breast:	n/a	chr1:227511338-227511346
4	BRCA1	chr1:227510798-227511758	Hela-S3	cervix:	n/a	n/a
5	FOS	chr1:227510930-227511727	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:227510974-227511158	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr1:227510856-227511852	Hela-S3	cervix:	n/a	n/a
8	GTF2F1	chr1:227510960-227511805	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr1:227510871-227511881	Hela-S3	cervix:	n/a	n/a
10	TCF7L2	chr1:227510920-227511321	Hela-S3	cervix:	n/a	n/a
11	STAT3	chr1:227510950-227511173	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr1:227510845-227511184	MCF10A-Er-Src	breast:	n/a	n/a
13	PRDM1	chr1:227510939-227511670	Hela-S3	cervix:	n/a	chr1:227511089-227511104
14	POLR2A	chr1:227510868-227511262	Hela-S3	cervix:	n/a	n/a
15	MYC	chr1:227510905-227511153	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr1:227510807-227511724	Hela-S3	cervix:	n/a	n/a
17	JUND	chr1:227510867-227511797	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr1:227511027-227511799	MCF-7	breast:	n/a	chr1:227511338-227511346
19	GATA3	chr1:227510946-227511557	MCF-7	breast:	n/a	chr1:227511338-227511346
20	STAT3	chr1:227510822-227511684	MCF10A-Er-Src	breast:	n/a	n/a
21	JUN	chr1:227510875-227511882	Hela-S3	cervix:	n/a	n/a
22	RCOR1	chr1:227510881-227511906	Hela-S3	cervix:	n/a	n/a
23	FOS	chr1:227510941-227511713	MCF10A-Er-Src	breast:	n/a	n/a
24	ZKSCAN1	chr1:227510912-227511797	Hela-S3	cervix:	n/a	n/a
25	RFX5	chr1:227510884-227511746	Hela-S3	cervix:	n/a	n/a
26	FOS	chr1:227510969-227511715	MCF10A-Er-Src	breast:	n/a	n/a
27	CEBPB	chr1:227510824-227512065	Hela-S3	cervix:	n/a	n/a
28	STAT3	chr1:227510833-227511200	MCF10A-Er-Src	breast:	n/a	n/a
29	RAD21	chr1:227510880-227511775	Hela-S3	cervix:	n/a	n/a
30	NFYB	chr1:227511001-227511972	Hela-S3	cervix:	n/a	chr1:227511084-227511094
31	FOS	chr1:227510889-227511733	MCF10A-Er-Src	breast:	n/a	n/a
32	MAZ	chr1:227510950-227511560	Hela-S3	cervix:	n/a	n/a
33	STAT3	chr1:227510817-227511774	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227510419..227513030-chr1:227581221..227583302,2	K562	blood:
2	chr1:227510624..227512509-chr1:227521394..227523406,2	K562	blood:
3	chr1:227509361..227511694-chr1:227523759..227526686,3	K562	blood:
4	chr1:227508074..227511114-chr1:227576547..227579179,3	K562	blood:
5	chr1:227510287..227513038-chr1:227518818..227521633,2	MCF-7	breast:

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000234277	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11800169	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11800364	1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	1.00[ASN][1000 genomes]
rs11801282	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802399	1.00[ASN][1000 genomes]
rs11803651	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11804181	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11804271	0.91[AMR][1000 genomes]
rs11804807	1.00[ASN][1000 genomes]
rs11806721	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807068	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808210	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808670	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808674	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808696	0.91[AMR][1000 genomes]
rs11809113	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11809905	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811210	1.00[ASN][1000 genomes]
rs11811620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811982	1.00[ASN][1000 genomes]
rs2718199	0.82[YRI][hapmap]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36055753	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41268741	1.00[ASN][1000 genomes]
rs41268743	1.00[ASN][1000 genomes]
rs41270147	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671926	1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7524967	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7530155	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547092	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660532	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11812048	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227507000-227515800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:227508400-227512200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:227509400-227511600	Enhancers	Stomach Mucosa	stomach
5	chr1:227509400-227516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:227509800-227511200	Active TSS	Duodenum Mucosa	Duodenum
7	chr1:227510000-227511800	Enhancers	Fetal Intestine Small	intestine
8	chr1:227510000-227511800	Enhancers	Pancreas	Pancrea
9	chr1:227510200-227511400	Enhancers	Fetal Intestine Large	intestine
10	chr1:227510200-227511600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:227510200-227511800	Enhancers	Gastric	stomach
12	chr1:227510400-227511400	Weak transcription	Colonic Mucosa	Colon
13	chr1:227510400-227511600	Enhancers	K562	blood
14	chr1:227510400-227516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:227510800-227511800	Enhancers	NHEK	skin
16	chr1:227510800-227512200	Flanking Active TSS	Hela-S3	cervix
17	chr1:227511000-227511200	Enhancers	Liver	Liver
18	chr1:227511000-227511800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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