Variant report

Variant	rs59472079
Chromosome Location	chr1:227510846-227510847
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr1:227510798-227511758	Hela-S3	cervix:	n/a	n/a
2	MYC	chr1:227510845-227511184	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr1:227510807-227511724	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr1:227510822-227511684	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr1:227510824-227512065	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr1:227510833-227511200	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:227510817-227511774	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10495254	0.89[ASN][1000 genomes]
rs11804613	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11804709	0.91[ASN][1000 genomes]
rs11805859	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11806180	0.91[ASN][1000 genomes]
rs11806188	0.91[ASN][1000 genomes]
rs11807620	0.91[ASN][1000 genomes]
rs11810471	0.91[ASN][1000 genomes]
rs12407020	0.91[ASN][1000 genomes]
rs12407033	0.91[ASN][1000 genomes]
rs1513615	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1546558	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1567802	0.81[EUR][1000 genomes]
rs1606550	0.84[AMR][1000 genomes]
rs16847612	0.89[ASN][1000 genomes]
rs16847617	0.89[ASN][1000 genomes]
rs16847618	0.89[ASN][1000 genomes]
rs16847625	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16847628	0.91[ASN][1000 genomes]
rs16847631	0.91[ASN][1000 genomes]
rs16847643	0.91[ASN][1000 genomes]
rs16847647	0.91[ASN][1000 genomes]
rs16847649	0.91[ASN][1000 genomes]
rs1849548	0.84[AMR][1000 genomes]
rs2063666	0.84[AMR][1000 genomes]
rs2102635	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2102637	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2102639	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2670447	0.84[AMR][1000 genomes]
rs2670450	0.81[EUR][1000 genomes]
rs2670451	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2718197	0.84[AMR][1000 genomes]
rs2718200	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2718216	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813945	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2813954	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2813963	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813973	0.82[AMR][1000 genomes]
rs2813975	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813982	0.84[AMR][1000 genomes]
rs3127003	0.83[AMR][1000 genomes]
rs35903393	0.84[AMR][1000 genomes]
rs3795456	0.89[ASN][1000 genomes]
rs4276876	0.89[ASN][1000 genomes]
rs4281297	0.89[ASN][1000 genomes]
rs4284230	0.89[ASN][1000 genomes]
rs4292922	0.89[ASN][1000 genomes]
rs4298700	0.89[ASN][1000 genomes]
rs4306096	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4344297	0.88[ASN][1000 genomes]
rs4415529	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4500280	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4545305	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4568795	0.87[ASN][1000 genomes]
rs4653490	0.89[ASN][1000 genomes]
rs4653492	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653493	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653494	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653809	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4653816	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653817	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653818	0.91[ASN][1000 genomes]
rs4653819	0.91[ASN][1000 genomes]
rs4653820	0.91[ASN][1000 genomes]
rs4653821	0.91[ASN][1000 genomes]
rs58912604	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59187211	0.89[ASN][1000 genomes]
rs59562576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59596249	0.91[ASN][1000 genomes]
rs60117206	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60592061	0.91[ASN][1000 genomes]
rs60693965	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs66523880	0.89[ASN][1000 genomes]
rs66738032	0.91[ASN][1000 genomes]
rs66765246	0.89[ASN][1000 genomes]
rs6691882	0.89[ASN][1000 genomes]
rs6693234	0.89[ASN][1000 genomes]
rs67070254	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs67723257	0.91[ASN][1000 genomes]
rs68043093	0.91[ASN][1000 genomes]
rs68077109	0.89[ASN][1000 genomes]
rs68133756	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72632805	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72632807	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72632810	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72632812	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72632813	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72632814	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72632818	0.89[ASN][1000 genomes]
rs72632819	0.89[ASN][1000 genomes]
rs72632820	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72632821	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72632822	0.89[ASN][1000 genomes]
rs72632823	0.91[ASN][1000 genomes]
rs72632824	0.91[ASN][1000 genomes]
rs72632825	0.91[ASN][1000 genomes]
rs7513776	0.90[ASN][1000 genomes]
rs7514796	0.89[ASN][1000 genomes]
rs7520769	0.91[ASN][1000 genomes]
rs7540775	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7541220	0.91[ASN][1000 genomes]
rs7541499	0.91[ASN][1000 genomes]
rs7549515	0.91[ASN][1000 genomes]
rs7549619	0.91[ASN][1000 genomes]
rs7552957	0.91[ASN][1000 genomes]
rs7554168	0.91[ASN][1000 genomes]
rs7556319	0.88[ASN][1000 genomes]
rs9426609	0.81[AMR][1000 genomes];0.81[EUR][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

No data

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	chr1:227507200-227511000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:227507200-227518200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:227508400-227512200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:227509400-227511600	Enhancers	Stomach Mucosa	stomach
6	chr1:227509400-227516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:227509800-227511200	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:227510000-227511800	Enhancers	Fetal Intestine Small	intestine
9	chr1:227510000-227511800	Enhancers	Pancreas	Pancrea
10	chr1:227510200-227511400	Enhancers	Fetal Intestine Large	intestine
11	chr1:227510200-227511600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr1:227510200-227511800	Enhancers	Gastric	stomach
13	chr1:227510400-227511400	Weak transcription	Colonic Mucosa	Colon
14	chr1:227510400-227511600	Enhancers	K562	blood
15	chr1:227510400-227516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:227510800-227511000	Flanking Active TSS	Liver	Liver
17	chr1:227510800-227511800	Enhancers	NHEK	skin
18	chr1:227510800-227512200	Flanking Active TSS	Hela-S3	cervix

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