Variant report

Variant	rs4952834
Chromosome Location	chr2:46777462-46777463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46776310..46779098-chr2:46785814..46787869,2	MCF-7	breast:
2	chr2:46769021..46773979-chr2:46774333..46777688,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1001745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12997164	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs13000560	0.81[AMR][1000 genomes]
rs13008088	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13013245	1.00[CHB][hapmap]
rs13020299	0.89[ASN][1000 genomes]
rs34050156	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34416415	0.96[ASN][1000 genomes]
rs35178974	0.93[ASN][1000 genomes]
rs35870739	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4142759	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]
rs4952831	1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs4952833	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs62134736	0.93[ASN][1000 genomes]
rs62134741	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62134759	0.82[AMR][1000 genomes]
rs7607308	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7607633	1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[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
rs4952834	SOCS5	cis	multi-tissue	Pritchard
rs4952834	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs4952834	ATP6V1E2	Cis_1M	lymphoblastoid	RTeQTL
rs4952834	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs4952834	CRIPT	cis	Frontal Cortex	GTEx
rs4952834	PIGF	cis	cerebellum	SCAN
rs4952834	CRIPT	cis	parietal	SCAN
rs4952834	ATP6V1E2	cis	Skin Sun Exposed Lower leg	GTEx
rs4952834	ATP6V1E2	cis	parietal	SCAN
rs4952834	ATP6V1E2	cis	multi-tissue	Pritchard
rs4952834	CRIPT	cis	multi-tissue	Pritchard
rs4952834	ATP6V1E2	cis	Whole Blood	GTEx
rs4952834	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs4952834	PIGF	cis	parietal	SCAN
rs4952834	ATP6V1E2	cis	lung	GTEx
rs4952834	CRIPT	cis	lymphoblastoid	seeQTL
rs4952834	ATP6V1E2	cis	Muscle Skeletal	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771000-46781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:46771200-46778000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:46771200-46780000	Enhancers	Psoas Muscle	Psoas
4	chr2:46771200-46781400	Weak transcription	NHEK	skin
5	chr2:46771200-46781600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:46771200-46781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:46771400-46778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:46771400-46780000	Genic enhancers	Fetal Muscle Leg	muscle
10	chr2:46771400-46781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
13	chr2:46771600-46781600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:46771600-46781600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:46771800-46777600	Enhancers	Brain Cingulate Gyrus	brain
16	chr2:46771800-46780000	Enhancers	Right Atrium	heart
17	chr2:46771800-46781400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:46771800-46781400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:46771800-46781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:46771800-46782000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:46771800-46782400	Weak transcription	HMEC	breast
22	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
23	chr2:46772000-46782600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:46772200-46780200	Genic enhancers	Left Ventricle	heart
25	chr2:46772200-46804000	Weak transcription	NH-A	brain
26	chr2:46772800-46777600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:46773000-46780200	Strong transcription	Osteobl	bone
28	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:46773400-46779800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:46773600-46778600	Genic enhancers	Brain Hippocampus Middle	brain
31	chr2:46774000-46778000	Genic enhancers	Fetal Stomach	stomach
32	chr2:46774000-46779800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:46774200-46777600	Strong transcription	Fetal Intestine Large	intestine
34	chr2:46774400-46778400	Enhancers	Thymus	Thymus
35	chr2:46774400-46782200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:46774600-46778600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:46774600-46778800	Genic enhancers	Right Ventricle	heart
38	chr2:46774600-46780000	Genic enhancers	Spleen	Spleen
39	chr2:46774800-46777800	Enhancers	Fetal Thymus	thymus
40	chr2:46774800-46781400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:46774800-46789200	Weak transcription	Pancreas	Pancrea
42	chr2:46775200-46778600	Weak transcription	HepG2	liver
43	chr2:46775200-46782400	Weak transcription	Fetal Lung	lung
44	chr2:46775200-46787200	Weak transcription	Gastric	stomach
45	chr2:46775200-46788600	Weak transcription	A549	lung
46	chr2:46775400-46778600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr2:46775400-46778600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:46775400-46779400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:46775400-46782600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:46775600-46778600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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