Variant report

Variant	rs34416415
Chromosome Location	chr2:46772306-46772307
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	FOXM1	chr2:46772197-46772873	GM12878	blood:	n/a	n/a
2	NFYB	chr2:46772136-46772449	K562	blood:	n/a	chr2:46772300-46772314 chr2:46772299-46772314 chr2:46772299-46772314
3	WRNIP1	chr2:46772154-46772339	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr2:46772290-46772795	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:46772297-46772487	K562	blood:	n/a	n/a
6	POLR2A	chr2:46768678-46773017	GM12892	blood:	n/a	n/a
7	POLR2A	chr2:46770477-46777171	GM12878	blood:	n/a	n/a
8	RFX5	chr2:46770190-46772854	SK-N-SH	brain:	n/a	chr2:46770339-46770347
9	CCNT2	chr2:46772148-46772769	K562	blood:	n/a	n/a
10	POLR2A	chr2:46770053-46772353	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:46770217-46773424	GM12878	blood:	n/a	n/a
12	ATF2	chr2:46772265-46772849	GM12878	blood:	n/a	n/a
13	RUNX3	chr2:46772095-46772992	GM12878	blood:	n/a	n/a
14	ATF2	chr2:46772300-46772848	GM12878	blood:	n/a	n/a
15	MXI1	chr2:46772199-46772874	GM12878	blood:	n/a	n/a
16	CEBPD	chr2:46772282-46772716	K562	blood:	n/a	n/a
17	RUNX3	chr2:46772103-46772951	GM12878	blood:	n/a	n/a
18	CUX1	chr2:46772108-46772664	K562	blood:	n/a	n/a
19	POLR2A	chr2:46768760-46773354	GM18505	blood:	n/a	n/a
20	MTA3	chr2:46771378-46773074	GM12878	blood:	n/a	n/a
21	RCOR1	chr2:46772043-46772913	K562	blood:	n/a	n/a
22	MXI1	chr2:46766247-46772861	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr2:46771967-46772852	GM12878	blood:	n/a	n/a
24	TEAD4	chr2:46772258-46772780	K562	blood:	n/a	n/a
25	CUX1	chr2:46772223-46772842	GM12878	blood:	n/a	n/a
26	NFYB	chr2:46772053-46772673	GM12878	blood:	n/a	chr2:46772300-46772314 chr2:46772299-46772314 chr2:46772299-46772314
27	NFIC	chr2:46772266-46772867	GM12878	blood:	n/a	n/a
28	CEBPB	chr2:46772217-46772521	K562	blood:	n/a	n/a
29	POLR2A	chr2:46770819-46773352	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46770485..46772962-chr2:46842113..46844264,3	MCF-7	breast:
2	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
3	chr2:46770414..46772957-chr2:46801807..46804486,2	MCF-7	breast:
4	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:
5	chr2:46767796..46769414-chr2:46769669..46772927,3	MCF-7	breast:
6	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:

Variant related genes	Relation type
ATP6V1E2	TF binding region
ENSG00000151665	Chromatin interaction
ENSG00000253515	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1001745	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12997164	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13008088	0.89[ASN][1000 genomes]
rs13020299	0.93[ASN][1000 genomes]
rs34050156	0.96[ASN][1000 genomes]
rs35178974	0.98[ASN][1000 genomes]
rs35870739	0.85[ASN][1000 genomes]
rs4142759	0.89[ASN][1000 genomes]
rs4952831	0.91[ASN][1000 genomes]
rs4952833	0.91[ASN][1000 genomes]
rs4952834	0.96[ASN][1000 genomes]
rs62134736	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62134741	0.89[ASN][1000 genomes]
rs7607308	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7607633	0.96[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs34416415	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs34416415	ATP6V1E2	cis	Whole Blood	GTEx
rs34416415	ATP6V1E2	cis	multi-tissue	Pritchard
rs34416415	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs34416415	ATP6V1E2	cis	Skin Sun Exposed Lower leg	GTEx
rs34416415	ATP6V1E2	cis	Esophagus Mucosa	GTEx
rs34416415	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs34416415	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs34416415	ATP6V1E2	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46769200-46772600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr2:46770200-46773000	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr2:46770600-46772800	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr2:46770600-46773000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr2:46770800-46772400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:46771000-46772800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:46771000-46774000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:46771000-46776600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:46771000-46781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:46771200-46772400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:46771200-46772600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:46771200-46772800	Flanking Active TSS	GM12878-XiMat	blood
13	chr2:46771200-46772800	Enhancers	K562	blood
14	chr2:46771200-46774200	Weak transcription	Liver	Liver
15	chr2:46771200-46774200	Weak transcription	Esophagus	oesophagus
16	chr2:46771200-46774400	Weak transcription	Ovary	ovary
17	chr2:46771200-46774400	Weak transcription	Thymus	Thymus
18	chr2:46771200-46774600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:46771200-46774800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:46771200-46778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:46771200-46780000	Enhancers	Psoas Muscle	Psoas
22	chr2:46771200-46781400	Weak transcription	NHEK	skin
23	chr2:46771200-46781600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:46771200-46781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:46771400-46772400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr2:46771400-46772400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:46771400-46772400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr2:46771400-46772400	Enhancers	Dnd41	blood
30	chr2:46771400-46772600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:46771400-46773200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr2:46771400-46774000	Weak transcription	Small Intestine	intestine
33	chr2:46771400-46774400	Weak transcription	Pancreas	Pancrea
34	chr2:46771400-46774800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr2:46771400-46777000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr2:46771400-46778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:46771400-46780000	Genic enhancers	Fetal Muscle Leg	muscle
38	chr2:46771400-46781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
41	chr2:46771600-46772400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:46771600-46772600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:46771600-46772800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:46771600-46773000	Enhancers	Spleen	Spleen
45	chr2:46771600-46773200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr2:46771600-46773400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:46771600-46773800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:46771600-46773800	Weak transcription	HepG2	liver
49	chr2:46771600-46774000	Weak transcription	Primary T cells from cord blood	blood
50	chr2:46771600-46774200	Weak transcription	Fetal Intestine Large	intestine

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