Variant report

Variant	rs358740
Chromosome Location	chr3:155466616-155466617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:155465273-155466975	U2OS	brain:	n/a	n/a
2	MAX	chr3:155466555-155466759	A549	lung:	n/a	n/a
3	JUN	chr3:155466612-155467019	HepG2	liver:	n/a	n/a
4	MAZ	chr3:155466459-155466859	HepG2	liver:	n/a	n/a
5	NR2F2	chr3:155466542-155467324	MCF-7	breast:	n/a	n/a
6	MAFK	chr3:155466528-155467111	HepG2	liver:	n/a	n/a
7	KAP1	chr3:155465596-155467159	HEK293	kidney:	n/a	n/a
8	ARID3A	chr3:155466486-155467223	HepG2	liver:	n/a	n/a
9	TEAD4	chr3:155466612-155467209	HepG2	liver:	n/a	n/a
10	JUND	chr3:155466571-155467052	HepG2	liver:	n/a	n/a
11	FOSL2	chr3:155466259-155467123	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:155460020..155464783-chr3:155465201..155469112,6	K562	blood:
2	chr3:155461411..155464910-chr3:155465071..155468362,4	MCF-7	breast:
3	chr3:155461079..155463376-chr3:155465033..155467779,3	MCF-7	breast:
4	chr3:155466610..155468263-chr3:155468525..155471754,3	MCF-7	breast:

No data

Variant related genes	Relation type
PLCH1	TF binding region
ENSG00000114805	Chromatin interaction
ENSG00000214919	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10936015	0.80[AMR][1000 genomes]
rs11923772	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13060077	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs173370	0.81[AMR][1000 genomes]
rs17349784	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs184836	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2201932	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2320190	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35769564	0.80[AFR][1000 genomes]
rs358714	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs358720	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358722	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs358736	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358738	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs358741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs358744	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358745	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs358746	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs358748	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35963081	0.80[AFR][1000 genomes]
rs369155	0.86[ASN][1000 genomes]
rs396797	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs400999	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426236	0.85[ASN][1000 genomes]
rs4680215	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680216	0.86[ASN][1000 genomes]
rs57183957	0.89[ASN][1000 genomes]
rs62284707	0.89[ASN][1000 genomes]
rs6441012	0.83[ASN][1000 genomes]
rs6774542	0.80[AFR][1000 genomes]
rs7619505	0.81[AMR][1000 genomes]
rs9866823	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv521244	chr3:155465491-155467069	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	nsv526490	chr3:155465932-155467069	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155463200-155467400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:155463800-155475200	Weak transcription	Left Ventricle	heart
3	chr3:155463800-155487800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
5	chr3:155464000-155476600	Weak transcription	Ovary	ovary
6	chr3:155464200-155469800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:155464200-155474800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
11	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
13	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:155464400-155467200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:155464400-155467400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:155464400-155467400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:155464600-155467200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:155464600-155467400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:155464600-155467400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:155465000-155467400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:155465000-155468200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:155465200-155466800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:155465200-155467000	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr3:155465400-155468000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr3:155465600-155467000	Enhancers	Fetal Brain Female	brain
28	chr3:155465600-155467400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:155465800-155467200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr3:155465800-155467200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:155465800-155468000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr3:155466000-155467000	Enhancers	Fetal Stomach	stomach
33	chr3:155466000-155467200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:155466000-155467200	Enhancers	Fetal Intestine Small	intestine
35	chr3:155466000-155467200	Enhancers	Fetal Kidney	kidney
36	chr3:155466000-155467400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:155466000-155468200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr3:155466200-155467200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:155466200-155467200	Enhancers	K562	blood
40	chr3:155466200-155467400	Flanking Active TSS	A549	lung
41	chr3:155466400-155467000	Enhancers	NHDF-Ad	bronchial
42	chr3:155466400-155467200	Enhancers	Fetal Intestine Large	intestine
43	chr3:155466400-155467400	Flanking Active TSS	HepG2	liver
44	chr3:155466400-155469600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:155466400-155484600	Weak transcription	Fetal Brain Male	brain
46	chr3:155466600-155466800	Bivalent Enhancer	Fetal Lung	lung
47	chr3:155466600-155467000	Enhancers	NH-A	brain
48	chr3:155466600-155467200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr3:155466600-155467200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr3:155466600-155467200	Enhancers	Hela-S3	cervix

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