Variant report

Variant	rs3780914
Chromosome Location	chr10:45935744-45935745
allele	C/T
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	BCL3	chr10:45935454-45935783	GM12878	blood:	n/a	chr10:45935545-45935558 chr10:45935544-45935553

Variant related genes	Relation type
ALOX5	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1073525	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs10751382	0.84[ASN][1000 genomes]
rs10751383	0.80[AMR][1000 genomes]
rs10793617	0.82[ASN][1000 genomes]
rs10900226	0.84[CHB][hapmap]
rs12765320	0.80[YRI][hapmap]
rs2291427	0.84[ASN][1000 genomes]
rs3780909	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949004	0.84[ASN][1000 genomes]
rs702365	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702366	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7080474	0.80[YRI][hapmap]
rs7087633	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7896175	0.84[CHB][hapmap]
rs7896431	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7920317	0.84[CHB][hapmap]
rs901681	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895107	chr10:45850300-45953767	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
5	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv895110	chr10:45912771-45953767	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription 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	2 gene(s)	inside rSNPs	diseases
7	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3780914	AGAP4	cis	Muscle Skeletal	GTEx
rs3780914	FXYD4	cis	parietal	SCAN
rs3780914	ANUBL1	cis	parietal	SCAN
rs3780914	AGAP4	cis	Whole Blood	GTEx
rs3780914	ANUBL1	cis	cerebellum	SCAN
rs3780914	AGAP4	cis	Artery Tibial	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45916600-45949200	Weak transcription	Gastric	stomach
2	chr10:45925000-45940600	Weak transcription	Fetal Intestine Small	intestine
3	chr10:45925000-45949200	Weak transcription	Lung	lung
4	chr10:45925800-45936200	Weak transcription	Placenta	Placenta
5	chr10:45928800-45951000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:45929200-45951600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr10:45930200-45938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:45934000-45938400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr10:45934000-45938600	Strong transcription	Primary B cells from cord blood	blood
10	chr10:45934000-45939400	Weak transcription	GM12878-XiMat	blood
11	chr10:45934000-45951200	Weak transcription	Esophagus	oesophagus
12	chr10:45934200-45938400	Strong transcription	Spleen	Spleen
13	chr10:45934200-45942000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr10:45934400-45941800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr10:45934600-45941400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr10:45934800-45936400	Enhancers	Thymus	Thymus
17	chr10:45934800-45936400	Weak transcription	K562	blood
18	chr10:45934800-45939200	Weak transcription	Pancreas	Pancrea
19	chr10:45935200-45936000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr10:45935200-45938200	Enhancers	Fetal Thymus	thymus
21	chr10:45935400-45943600	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr10:45935600-45936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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