Variant report

Variant	rs2484296
Chromosome Location	chr10:43135220-43135221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
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	chr10:43132448-43135369	MCF10A-Er-Src	breast:	n/a	n/a
2	SPI1	chr10:43135187-43135442	GM12878	blood:	n/a	n/a
3	SPI1	chr10:43135153-43135473	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:43133794..43135524-chr11:62607798..62609419,2	MCF-7	breast:
2	chr10:43132257..43135644-chr10:43275563..43280155,11	MCF-7	breast:
3	chr10:43046145..43048386-chr10:43132522..43135382,4	MCF-7	breast:
4	chr10:43125083..43130093-chr10:43132029..43136060,7	K562	blood:
5	chr10:43132020..43136600-chr10:43277441..43279853,5	MCF-7	breast:
6	chr10:43043951..43049889-chr10:43132519..43135803,5	K562	blood:
7	chr10:43132026..43134878-chr10:43134908..43136583,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF33B	TF binding region
ENSG00000272373	TF binding region
ENSG00000272373	Chromatin interaction
ENSG00000196693	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000165733	Chromatin interaction
ENSG00000234420	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1147916	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1147917	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1147918	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1147919	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255414	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs209394	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2473112	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2473115	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2473116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504025	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505886	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2484296	LINC00839	cis	Artery Aorta	GTEx
rs2484296	LINC00839	cis	Artery Tibial	GTEx
rs2484296	LINC00839	cis	lung	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43134400-43136200	Weak transcription	Pancreas	Pancrea
2	chr10:43134400-43136400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:43134400-43136400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr10:43134400-43141600	Weak transcription	Gastric	stomach
5	chr10:43134600-43135400	Enhancers	Liver	Liver
6	chr10:43134600-43135600	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:43134600-43136000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:43134600-43136000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr10:43134600-43136200	Weak transcription	Placenta	Placenta
10	chr10:43134600-43136200	Weak transcription	Stomach Mucosa	stomach
11	chr10:43134600-43138400	Enhancers	Fetal Intestine Small	intestine
12	chr10:43134600-43140200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr10:43134600-43142200	Weak transcription	Aorta	Aorta
14	chr10:43134800-43135400	Enhancers	Primary B cells from cord blood	blood
15	chr10:43134800-43135400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr10:43134800-43135400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr10:43134800-43135400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:43134800-43136000	Weak transcription	NHEK	skin
19	chr10:43134800-43136200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:43134800-43137000	Weak transcription	A549	lung
21	chr10:43134800-43137600	Enhancers	Fetal Intestine Large	intestine
22	chr10:43134800-43141600	Weak transcription	Fetal Kidney	kidney
23	chr10:43134800-43143200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:43135000-43135400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:43135000-43135400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr10:43135000-43135400	Enhancers	Dnd41	blood
27	chr10:43135000-43136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:43135000-43136000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr10:43135200-43135600	Enhancers	K562	blood
30	chr10:43135200-43136200	Weak transcription	HepG2	liver
31	chr10:43135200-43140000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:43135200-43141800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr10:43135200-43145600	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links