Variant report

Variant	rs2839680
Chromosome Location	chr10:44883630-44883631
allele	A/G
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	RAD21	chr10:44883521-44883639	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:44882608..44885734-chr10:44887032..44891125,3	MCF-7	breast:

Variant related genes	Relation type
CXCL12	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11239028	0.83[EUR][1000 genomes]
rs17156287	0.96[ASN][1000 genomes]
rs17482472	0.91[ASN][1000 genomes]
rs17540492	0.85[AFR][1000 genomes]
rs17879548	0.96[ASN][1000 genomes]
rs17880358	0.96[ASN][1000 genomes]
rs17880777	0.85[AFR][1000 genomes]
rs17880863	0.96[ASN][1000 genomes]
rs17881575	0.96[ASN][1000 genomes]
rs17883339	0.95[ASN][1000 genomes]
rs17885289	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs197452	0.96[ASN][1000 genomes]
rs266088	0.80[ASN][1000 genomes]
rs2839679	0.90[AFR][1000 genomes]
rs2839682	1.00[ASN][1000 genomes]
rs2839683	0.84[AFR][1000 genomes]
rs2839684	0.96[ASN][1000 genomes]
rs2839686	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839687	0.84[AFR][1000 genomes]
rs2861441	0.90[AFR][1000 genomes]
rs2861442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780891	0.96[ASN][1000 genomes]
rs4520554	0.85[AFR][1000 genomes]
rs7082547	0.90[AFR][1000 genomes]
rs7088876	0.84[AFR][1000 genomes]
rs7092453	0.84[AFR][1000 genomes]
rs7093481	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790861	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790862	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728142	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv895090	chr10:44874867-44884959	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv895091	chr10:44875040-44888130	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv895092	chr10:44875166-44884959	Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv895093	chr10:44876461-44884959	Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv895094	chr10:44876499-44884959	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv895095	chr10:44876586-44884959	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv895096	chr10:44876586-44886206	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv895097	chr10:44876586-44888130	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv895099	chr10:44878114-44884959	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv895100	chr10:44878835-44884959	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv3375268	chr10:44878846-44883969	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44881000-44884600	Weak transcription	Psoas Muscle	Psoas
2	chr10:44881000-44884600	Weak transcription	NHDF-Ad	bronchial
3	chr10:44881200-44884200	Weak transcription	Liver	Liver
4	chr10:44881200-44884200	Weak transcription	Right Atrium	heart
5	chr10:44881200-44884400	Weak transcription	Left Ventricle	heart
6	chr10:44882000-44884200	Weak transcription	Adipose Nuclei	Adipose
7	chr10:44882400-44884000	Weak transcription	Fetal Heart	heart
8	chr10:44882400-44884200	Weak transcription	Right Ventricle	heart
9	chr10:44882400-44884800	Weak transcription	Pancreas	Pancrea
10	chr10:44882600-44884600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:44882600-44885800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:44882600-44885800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:44882600-44885800	Weak transcription	HepG2	liver
14	chr10:44882600-44885800	Weak transcription	Osteobl	bone
15	chr10:44882800-44885800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:44882800-44885800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:44883200-44883800	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