Variant report

Variant	rs12333409
Chromosome Location	chr7:26782926-26782927
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	MAFK	chr7:26782892-26783190	HepG2	liver:	n/a	chr7:26783023-26783038 chr7:26783025-26783034
2	MAFK	chr7:26782861-26783179	IMR90	lung:	n/a	chr7:26783023-26783038 chr7:26783025-26783034
3	GATA3	chr7:26782795-26782939	SH-SY5Y	brain:	n/a	n/a
4	MAFK	chr7:26782909-26783162	K562	blood:	n/a	chr7:26783023-26783038 chr7:26783025-26783034
5	MAFF	chr7:26782870-26783171	K562	blood:	n/a	n/a
6	MAFK	chr7:26782868-26783166	HepG2	liver:	n/a	chr7:26783023-26783038 chr7:26783025-26783034

Variant related genes	Relation type
SKAP2	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10085562	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10226612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10227575	0.88[EUR][1000 genomes]
rs10231080	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10238067	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10246300	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10246483	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246578	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10247117	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10248232	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10250097	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10250304	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10250321	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10251817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252268	0.86[EUR][1000 genomes]
rs10254460	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254467	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257057	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10261927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10262212	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10262527	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10262797	0.85[EUR][1000 genomes]
rs10265607	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10271393	0.93[EUR][1000 genomes]
rs10277060	0.88[EUR][1000 genomes]
rs10280403	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1030647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10486473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486474	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486480	0.85[EUR][1000 genomes]
rs10486481	0.86[EUR][1000 genomes]
rs12155150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12333690	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12334154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548482	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17154428	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17154538	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17310268	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17310851	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17310907	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17313134	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17323962	0.81[EUR][1000 genomes]
rs17370293	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17371905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195902	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28414527	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465643	0.88[EUR][1000 genomes]
rs28645143	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28781274	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34616067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141345	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4141346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59738260	0.86[ASN][1000 genomes]
rs61636979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67719086	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6950668	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954621	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6961653	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069515	0.83[EUR][1000 genomes]
rs73073794	0.91[EUR][1000 genomes]
rs73079514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779269	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7781784	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782851	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7783807	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784380	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786308	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7786456	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7806174	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9648328	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9648329	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9648332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9648333	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018125	chr7:26745074-26789814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26750400-26812000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:26754800-26783200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr7:26776200-26800000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:26779200-26783600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:26779200-26787200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:26779600-26810600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:26779800-26798600	Weak transcription	Primary B cells from cord blood	blood
8	chr7:26779800-26809000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:26780200-26783400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:26780200-26784200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:26780800-26797400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr7:26781000-26809200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:26782800-26783000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr7:26782800-26783200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:26782800-26783400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:26782800-26783600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links