Variant report

Variant	rs4142759
Chromosome Location	chr2:46783890-46783891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46782460..46784571-chr2:46785094..46788093,2	K562	blood:
2	chr2:46781985..46785151-chr2:46792596..46794911,4	MCF-7	breast:
3	chr2:46769633..46771937-chr2:46780333..46785033,5	MCF-7	breast:
4	chr2:46780322..46782811-chr2:46783470..46785498,2	K562	blood:

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1001745	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs12997164	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs13000560	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13008088	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013245	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs13020299	0.83[ASN][1000 genomes]
rs17818315	0.95[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs34050156	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34416415	0.89[ASN][1000 genomes]
rs35178974	0.87[ASN][1000 genomes]
rs35625984	0.89[EUR][1000 genomes]
rs35870739	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952831	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4952833	1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4952834	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56086832	0.87[EUR][1000 genomes]
rs62134736	0.87[ASN][1000 genomes]
rs62134741	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134759	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607308	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7607633	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[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	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
9	nsv9713	chr2:46775356-46790566	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4142759	ATP6V1E2	cis	Esophagus Muscularis	GTEx
rs4142759	CRIPT	cis	lymphoblastoid	seeQTL
rs4142759	CRIPT	cis	parietal	SCAN
rs4142759	RHOQ	cis	cerebellum	SCAN
rs4142759	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs4142759	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs4142759	PIGF	cis	lymphoblastoid	seeQTL
rs4142759	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs4142759	ATP6V1E2	cis	lung	GTEx
rs4142759	CRIPT	cis	Temporal Cortex	GTEx
rs4142759	CRIPT	cis	Frontal Cortex	GTEx
rs4142759	PIGF	cis	parietal	SCAN
rs4142759	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs4142759	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs4142759	ATP6V1E2	cis	parietal	SCAN
rs4142759	PIGF	cis	cerebellum	SCAN
rs4142759	CRIPT	cis	cerebellum	SCAN

Chromatin state (count:105 , 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	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
4	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
5	chr2:46772200-46804000	Weak transcription	NH-A	brain
6	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:46774800-46789200	Weak transcription	Pancreas	Pancrea
8	chr2:46775200-46787200	Weak transcription	Gastric	stomach
9	chr2:46775200-46788600	Weak transcription	A549	lung
10	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
11	chr2:46776400-46784800	Weak transcription	Dnd41	blood
12	chr2:46776400-46789000	Weak transcription	Primary T cells from cord blood	blood
13	chr2:46776600-46784800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr2:46776600-46785000	Weak transcription	Liver	Liver
15	chr2:46776600-46785200	Weak transcription	Small Intestine	intestine
16	chr2:46776600-46786000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:46776600-46789000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:46776800-46794600	Weak transcription	Ovary	ovary
19	chr2:46777000-46785000	Weak transcription	HSMM	muscle
20	chr2:46777000-46788600	Weak transcription	Colonic Mucosa	Colon
21	chr2:46777000-46788800	Weak transcription	HSMMtube	muscle
22	chr2:46777000-46789200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr2:46777600-46785200	Weak transcription	Fetal Intestine Large	intestine
24	chr2:46778400-46788600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:46778600-46784800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:46778600-46786000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:46779000-46790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:46779000-46790600	Weak transcription	K562	blood
29	chr2:46779800-46788400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:46779800-46794600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:46780000-46785200	Weak transcription	Aorta	Aorta
32	chr2:46780000-46785200	Weak transcription	Fetal Intestine Small	intestine
33	chr2:46780000-46785600	Weak transcription	Thymus	Thymus
34	chr2:46780200-46784800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:46780800-46784400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:46781400-46784000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr2:46781400-46784000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:46781400-46784200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:46781400-46784400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr2:46781600-46784000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:46781800-46785400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:46782000-46786600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:46782200-46785200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:46782200-46798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:46782400-46784400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:46782400-46785200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr2:46782400-46786200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:46782400-46786600	Weak transcription	Lung	lung
49	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
50	chr2:46782600-46785000	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links