Variant report

Variant	rs4953401
Chromosome Location	chr2:46799248-46799249
allele	G/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	ZNF384	chr2:46799130-46799316	K562	blood:	n/a	n/a
2	GATA2	chr2:46799128-46799321	SH-SY5Y	brain:	n/a	chr2:46799220-46799236 chr2:46799222-46799234

No.	Distal block	Cell Line	Cell type
1	chr2:46798350..46800285-chr2:47402187..47404172,2	K562	blood:
2	chr2:46797930..46799868-chr2:46827992..46829554,2	MCF-7	breast:
3	chr2:46795284..46799480-chr2:46800888..46803285,4	K562	blood:
4	chr2:46786591..46788548-chr2:46799220..46801395,2	K562	blood:
5	chr2:46796652..46799602-chr2:46801642..46804001,3	MCF-7	breast:
6	chr2:46681213..46683029-chr2:46797843..46800653,2	K562	blood:

Variant related genes	Relation type
RHOQ	TF binding region
ENSG00000119729	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13013245	0.86[ASN][1000 genomes]
rs35625984	0.86[ASN][1000 genomes]
rs56086832	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers 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	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4953401	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs4953401	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs4953401	ATP6V1E2	cis	lung	GTEx
rs4953401	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs4953401	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:46772200-46804000	Weak transcription	NH-A	brain
3	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
5	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
6	chr2:46782800-46803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:46783200-46803000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:46784000-46802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:46785600-46803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:46786800-46805200	Weak transcription	Small Intestine	intestine
15	chr2:46787200-46799800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:46787800-46806600	Weak transcription	Gastric	stomach
17	chr2:46789400-46811200	Weak transcription	Colonic Mucosa	Colon
18	chr2:46789800-46805800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:46789800-46807000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:46790000-46803400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:46790000-46803800	Weak transcription	Primary T cells from cord blood	blood
22	chr2:46790000-46807200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:46790000-46842000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:46790200-46803400	Weak transcription	A549	lung
25	chr2:46790200-46807000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:46790200-46807400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:46790600-46803800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:46790600-46806200	Weak transcription	Dnd41	blood
29	chr2:46792200-46809200	Weak transcription	Esophagus	oesophagus
30	chr2:46793000-46803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:46793000-46806400	Weak transcription	Lung	lung
32	chr2:46793200-46806200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:46793200-46806200	Weak transcription	Aorta	Aorta
34	chr2:46793400-46799800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:46794000-46800200	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:46794400-46799600	Enhancers	Fetal Thymus	thymus
37	chr2:46794600-46800000	Enhancers	Ovary	ovary
38	chr2:46795000-46802400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:46796000-46800800	Enhancers	Left Ventricle	heart
40	chr2:46796000-46801200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:46796000-46802000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:46796000-46807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:46796000-46812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:46796200-46800400	Enhancers	Colon Smooth Muscle	Colon
45	chr2:46796200-46806400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:46796200-46807800	Weak transcription	Stomach Mucosa	stomach
47	chr2:46796400-46802000	Weak transcription	HSMM	muscle
48	chr2:46796400-46803800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:46796400-46806400	Weak transcription	Placenta	Placenta
50	chr2:46796400-46807000	Weak transcription	Spleen	Spleen

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