Variant report

Variant	rs12673259
Chromosome Location	chr7:112051879-112051880
allele	A/C
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:8)
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	CTCF	chr7:112050499-112051895	A549	lung:	n/a	chr7:112051633-112051642
2	CTCF	chr7:112050711-112051887	SK-N-SH	brain:	n/a	chr7:112051633-112051642
3	RAD21	chr7:112050034-112052306	SK-N-SH	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:112049730..112052171-chr7:112053926..112056276,3	K562	blood:
2	chr7:112045125..112048422-chr7:112049738..112053855,5	K562	blood:
3	chr7:112050573..112053136-chr7:112089164..112091552,2	MCF-7	breast:
4	chr7:112048671..112054554-chr7:112088966..112092653,8	K562	blood:
5	chr7:111403379..111404358-chr7:112051159..112051887,3	MCF-7	breast:
6	chr7:112050774..112053695-chr7:112073947..112076333,2	K562	blood:
7	chr7:112049693..112052446-chr7:112089375..112092902,3	K562	blood:
8	chr7:112051238..112053639-chr7:112090198..112091815,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226851	TF binding region
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10238141	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs10272126	0.82[CEU][hapmap]
rs10953710	0.88[CEU][hapmap]
rs10953711	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs11761807	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs11763356	0.83[ASN][1000 genomes]
rs11763588	0.82[CEU][hapmap]
rs11763768	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11768608	0.82[CEU][hapmap]
rs11768891	0.82[JPT][hapmap]
rs11769219	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs11773393	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs12666911	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230061	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs17159389	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs17159446	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs1985929	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2188534	0.84[ASN][1000 genomes]
rs2396536	0.85[CEU][hapmap]
rs2520470	0.84[ASN][1000 genomes]
rs2520471	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2520473	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2520474	0.84[ASN][1000 genomes]
rs2520475	0.84[ASN][1000 genomes]
rs2523029	0.93[ASN][1000 genomes]
rs2523030	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523035	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2523037	0.86[ASN][1000 genomes]
rs2523038	0.86[ASN][1000 genomes]
rs2523039	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2523041	0.86[ASN][1000 genomes]
rs2708588	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2708590	0.93[ASN][1000 genomes]
rs2708592	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708594	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2708595	0.90[ASN][1000 genomes]
rs2708597	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708598	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708603	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708604	0.86[ASN][1000 genomes]
rs2708605	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3109114	0.82[CEU][hapmap]
rs34171150	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823515	0.82[ASN][1000 genomes]
rs41281063	0.83[ASN][1000 genomes]
rs4464880	0.88[CEU][hapmap]
rs4730516	0.82[JPT][hapmap]
rs55662318	0.87[ASN][1000 genomes]
rs56969420	0.86[ASN][1000 genomes]
rs6949164	0.82[JPT][hapmap]
rs6955231	0.88[CEU][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6978927	0.82[CEU][hapmap]
rs7795336	0.88[CEU][hapmap];0.82[JPT][hapmap]

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	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
3	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112046000-112060400	Weak transcription	Brain Angular Gyrus	brain
2	chr7:112050600-112052800	Enhancers	HepG2	liver
3	chr7:112051000-112053000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:112051200-112054800	Weak transcription	Fetal Lung	lung
5	chr7:112051400-112052000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr7:112051400-112053400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:112051400-112055400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr7:112051600-112052000	Enhancers	HUVEC	blood vessel
9	chr7:112051600-112053400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:112051600-112055200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr7:112051600-112055200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:112051600-112062000	Weak transcription	Right Atrium	heart
13	chr7:112051800-112059800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:112051800-112060400	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:112051800-112060400	Weak transcription	Brain Inferior Temporal Lobe	brain

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