Variant report

Variant	rs4384837
Chromosome Location	chr2:46789514-46789515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46788951..46790463-chr2:46844313..46846805,2	K562	blood:
2	chr2:46787456..46790384-chr2:46790520..46794497,4	K562	blood:
3	chr2:46778318..46780393-chr2:46788541..46791155,3	K562	blood:
4	chr2:46778318..46780093-chr2:46788541..46791155,2	K562	blood:
5	chr2:46787456..46790451-chr2:46790520..46794497,4	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12105801	0.81[EUR][1000 genomes]
rs12712976	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13413254	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13420857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1451152	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1451153	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs1901263	0.80[MEX][hapmap]
rs2305350	0.80[CHB][hapmap];0.81[GIH][hapmap]
rs6725948	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6734476	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6750698	0.87[AMR][1000 genomes];0.84[EUR][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4384837	PIGF	Cis_1M	lymphoblastoid	RTeQTL
rs4384837	RHOQ	cis	cerebellum	SCAN
rs4384837	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs4384837	CRIPT	cis	multi-tissue	Pritchard
rs4384837	PIGF	cis	lymphoblastoid	seeQTL
rs4384837	PIGF	cis	multi-tissue	Pritchard
rs4384837	CRIPT	cis	Temporal Cortex	GTEx
rs4384837	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs4384837	PIGF	cis	cerebellum	SCAN
rs4384837	CRIPT	cis	Lymphoblastoid	GTEx
rs4384837	CRIPT	cis	Frontal Cortex	GTEx
rs4384837	CRIPT	cis	parietal	SCAN
rs4384837	CRIPT	cis	lymphoblastoid	seeQTL
rs4384837	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs4384837	PIGF	cis	parietal	SCAN

Chromatin state (count:110 , 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	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
8	chr2:46776800-46794600	Weak transcription	Ovary	ovary
9	chr2:46779000-46790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:46779000-46790600	Weak transcription	K562	blood
11	chr2:46779800-46794600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:46782200-46798400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:46782400-46806600	Weak transcription	Brain Germinal Matrix	brain
14	chr2:46782800-46803600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:46783000-46792000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:46783000-46795600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:46783000-46796800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:46783000-46807200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:46783200-46791600	Weak transcription	Esophagus	oesophagus
20	chr2:46783200-46795400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:46783200-46803000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:46783600-46838000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:46784000-46802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:46785200-46790800	Genic enhancers	Monocytes-CD14+_RO01746	blood
25	chr2:46785400-46789600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:46785400-46789600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr2:46785400-46791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:46785400-46792000	Weak transcription	Aorta	Aorta
29	chr2:46785400-46796000	Weak transcription	HSMM	muscle
30	chr2:46785400-46798400	Weak transcription	Liver	Liver
31	chr2:46785400-46807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:46785400-46809400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr2:46785600-46796400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:46785600-46803800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:46785800-46792600	Weak transcription	Fetal Lung	lung
36	chr2:46786000-46793000	Enhancers	Right Atrium	heart
37	chr2:46786200-46789800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:46786200-46793000	Strong transcription	NHLF	lung
39	chr2:46786600-46795000	Strong transcription	Fetal Stomach	stomach
40	chr2:46786800-46790200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:46786800-46791000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:46786800-46805200	Weak transcription	Small Intestine	intestine
43	chr2:46787200-46790400	Strong transcription	Osteobl	bone
44	chr2:46787200-46791600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:46787200-46799800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:46787800-46806600	Weak transcription	Gastric	stomach
47	chr2:46788400-46789800	Genic enhancers	Primary monocytes fromperipheralblood	blood
48	chr2:46788400-46790600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr2:46788400-46790600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr2:46788400-46790800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood

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