Variant report

Variant	rs2240766
Chromosome Location	chr12:4677255-4677256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:4650790..4653487-chr12:4676883..4679720,2	K562	blood:

Variant related genes	Relation type
ENSG00000111247	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10744652	0.81[ASN][1000 genomes]
rs10774242	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774243	0.87[ASN][1000 genomes]
rs11063237	0.83[TSI][hapmap]
rs11063240	0.87[EUR][1000 genomes]
rs12368152	0.87[EUR][1000 genomes]
rs4766252	0.86[ASN][1000 genomes]
rs4766253	0.89[ASN][1000 genomes]
rs4766254	0.89[ASN][1000 genomes]
rs4766255	0.89[ASN][1000 genomes]
rs4766258	0.87[ASN][1000 genomes]
rs4766259	0.87[ASN][1000 genomes]
rs717568	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs7957831	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1038332	chr12:4627992-4689300	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541362	chr12:4627992-4689300	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2240766	CCDC77	cis	cerebellum	SCAN
rs2240766	KCNA5	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4670200-4679600	Weak transcription	Hela-S3	cervix
2	chr12:4670400-4679200	Weak transcription	A549	lung
3	chr12:4671800-4680400	Weak transcription	HUVEC	blood vessel
4	chr12:4671800-4683400	Weak transcription	Thymus	Thymus
5	chr12:4672000-4680000	Weak transcription	Brain Anterior Caudate	brain
6	chr12:4672000-4682600	Weak transcription	Spleen	Spleen
7	chr12:4672400-4685000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:4672800-4679600	Weak transcription	Fetal Thymus	thymus
9	chr12:4672800-4680000	Weak transcription	Brain Substantia Nigra	brain
10	chr12:4673400-4692200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:4673600-4678000	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:4673800-4677600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr12:4674400-4677600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:4675200-4677600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:4675400-4677600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr12:4675400-4680000	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:4675800-4684000	Weak transcription	Lung	lung
18	chr12:4676000-4679000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:4676200-4677400	Enhancers	K562	blood
20	chr12:4676400-4677400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:4676400-4677400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:4676800-4678200	Strong transcription	Dnd41	blood
23	chr12:4677000-4677400	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr12:4677000-4677800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:4677000-4678200	Enhancers	GM12878-XiMat	blood
26	chr12:4677200-4677400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:4677200-4677400	Enhancers	Duodenum Mucosa	Duodenum
28	chr12:4677200-4679000	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links