Variant report

Variant	rs3742945
Chromosome Location	chr14:20770036-20770037
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	chr14:20770034-20770924	K562	blood:	n/a	chr14:20770379-20770389
2	ATF1	chr14:20769953-20770557	K562	blood:	n/a	n/a
3	CUX1	chr14:20769996-20770530	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:20768802..20770560-chr14:20773922..20776589,2	MCF-7	breast:
2	chr14:20767452..20770221-chr14:20798521..20800836,2	K562	blood:
3	chr14:20769637..20772155-chr14:20772254..20774173,3	K562	blood:
4	chr14:20765245..20767756-chr14:20769308..20771305,2	K562	blood:
5	chr14:20769637..20771954-chr14:20772645..20774173,2	K562	blood:

Variant related genes	Relation type
ENSG00000258459	TF binding region
ENSG00000258459	Chromatin interaction
ENSG00000100814	Chromatin interaction
ENSG00000136319	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10873395	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297616	0.87[CHD][hapmap]
rs2318864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3093890	0.87[CHD][hapmap]
rs3093907	0.87[CHD][hapmap]
rs3825766	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981148	0.81[MEX][hapmap]
rs4981951	0.81[MEX][hapmap]
rs61995501	0.90[EUR][1000 genomes]
rs6575135	0.91[CHD][hapmap]
rs7155699	0.91[CHD][hapmap];0.83[JPT][hapmap]
rs8009242	0.80[CEU][hapmap];0.87[CHD][hapmap]
rs8022565	0.91[CHD][hapmap]
rs945459	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1043938	chr14:20427182-20776276	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv541971	chr14:20427182-20776276	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
6	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
7	nsv869984	chr14:20732655-20776216	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
9	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3742945	TTC5	cis	parietal	SCAN
rs3742945	CCNB1IP1	cis	parietal	SCAN
rs3742945	CCNB1IP1	cis	cerebellum	SCAN
rs3742945	PARP2	cis	parietal	SCAN
rs3742945	TTC5	cis	cerebellum	SCAN
rs3742945	RPPH1	cis	multi-tissue	Pritchard
rs3742945	PARP2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20746600-20773200	Weak transcription	Stomach Mucosa	stomach
2	chr14:20749200-20773400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:20754400-20770200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr14:20754400-20770800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr14:20754600-20770400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr14:20754600-20770400	Strong transcription	Dnd41	blood
7	chr14:20754800-20770200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr14:20754800-20770400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr14:20754800-20770400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:20754800-20770400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:20754800-20770400	Strong transcription	Adipose Nuclei	Adipose
12	chr14:20754800-20770400	Strong transcription	Liver	Liver
13	chr14:20754800-20770400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:20754800-20770600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr14:20755000-20770400	Strong transcription	Primary T cells from cord blood	blood
16	chr14:20755000-20770400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr14:20755000-20770600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr14:20755200-20770200	Strong transcription	Primary hematopoietic stem cells	blood
19	chr14:20755200-20770200	Strong transcription	Aorta	Aorta
20	chr14:20755200-20770200	Strong transcription	Fetal Brain Female	brain
21	chr14:20755200-20770200	Strong transcription	Left Ventricle	heart
22	chr14:20755200-20770200	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr14:20755200-20770400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:20755200-20770400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr14:20755200-20770400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr14:20755400-20770200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:20755400-20770200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr14:20755400-20770200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr14:20755400-20770200	Strong transcription	Ovary	ovary
30	chr14:20756400-20770200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:20758000-20773200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:20758400-20770200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:20758400-20770400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:20758600-20770400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr14:20759000-20770400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:20759000-20770400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr14:20759000-20770400	Strong transcription	Fetal Intestine Large	intestine
38	chr14:20759000-20770400	Strong transcription	Fetal Muscle Leg	muscle
39	chr14:20759200-20770200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:20759600-20770600	Strong transcription	Primary B cells from cord blood	blood
41	chr14:20759800-20770400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr14:20760200-20770200	Strong transcription	Fetal Lung	lung
43	chr14:20760200-20772800	Weak transcription	Fetal Heart	heart
44	chr14:20760600-20770400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr14:20760800-20770400	Strong transcription	Brain Hippocampus Middle	brain
46	chr14:20760800-20770400	Strong transcription	Colon Smooth Muscle	Colon
47	chr14:20761400-20770200	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr14:20763600-20772400	Weak transcription	Hela-S3	cervix
49	chr14:20764200-20770200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr14:20764200-20773400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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