Variant report

Variant	rs2314338
Chromosome Location	chr17:38344485-38344486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38168785..38171760-chr17:38343651..38347238,3	K562	blood:
2	chr17:38343572..38346037-chr17:38346737..38348238,2	K562	blood:
3	chr17:38343298..38345399-chr17:38347624..38349920,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108342	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000265799	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11078940	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs12103921	0.82[ASN][1000 genomes]
rs16965666	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs16965687	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2071570	0.89[MEX][hapmap]
rs2280400	0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs28537537	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs34223321	0.83[ASN][1000 genomes]
rs3744806	0.83[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4077125	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs45567834	0.83[ASN][1000 genomes]
rs4566234	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs55772196	0.82[ASN][1000 genomes]
rs55991953	0.81[ASN][1000 genomes]
rs56013073	0.83[ASN][1000 genomes]
rs6503539	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs7211770	0.89[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs72836633	0.81[ASN][1000 genomes]
rs7359537	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7405635	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap]
rs8066144	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs8073925	0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs8082192	0.83[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs939347	0.83[MEX][hapmap]
rs9892946	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9892973	0.83[ASN][1000 genomes]
rs9893520	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9901109	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs9904021	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9907683	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9908034	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9908257	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs9908354	0.81[ASN][1000 genomes]
rs9916460	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs9916782	0.83[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2314338	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38333200-38347000	Weak transcription	Brain Substantia Nigra	brain
2	chr17:38333600-38347000	Weak transcription	Fetal Lung	lung
3	chr17:38334000-38347000	Weak transcription	HUVEC	blood vessel
4	chr17:38334200-38346800	Weak transcription	Spleen	Spleen
5	chr17:38334200-38347000	Weak transcription	GM12878-XiMat	blood
6	chr17:38334200-38347400	Weak transcription	Aorta	Aorta
7	chr17:38334400-38346800	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:38334400-38346800	Weak transcription	Ovary	ovary
9	chr17:38334600-38345200	Weak transcription	Right Ventricle	heart
10	chr17:38334600-38346600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr17:38334600-38346800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:38335000-38345000	Weak transcription	Brain Germinal Matrix	brain
13	chr17:38335000-38345400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr17:38335000-38346400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr17:38335200-38346600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:38335200-38346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:38335200-38346800	Weak transcription	Thymus	Thymus
18	chr17:38335200-38347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:38335200-38347800	Weak transcription	Small Intestine	intestine
20	chr17:38335400-38346800	Weak transcription	Fetal Brain Male	brain
21	chr17:38335400-38347000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:38336400-38347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr17:38336400-38347000	Weak transcription	NHDF-Ad	bronchial
24	chr17:38336400-38347000	Weak transcription	NHLF	lung
25	chr17:38336600-38346600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr17:38336600-38346600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:38336600-38346800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:38336800-38347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:38337000-38346400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr17:38337000-38346800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:38337000-38347000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:38337000-38347000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr17:38337000-38347000	Weak transcription	Osteobl	bone
34	chr17:38337200-38344600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr17:38337200-38345000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:38337200-38346600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:38337200-38346600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:38337200-38346600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:38337200-38347000	Weak transcription	Brain Angular Gyrus	brain
40	chr17:38337200-38347200	Weak transcription	NH-A	brain
41	chr17:38337400-38346600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr17:38337400-38346800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr17:38337600-38347000	Weak transcription	HSMM	muscle
44	chr17:38337800-38344600	Weak transcription	HSMMtube	muscle
45	chr17:38337800-38344800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:38337800-38346600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:38337800-38347000	Weak transcription	Lung	lung
48	chr17:38337800-38347000	Weak transcription	Pancreas	Pancrea
49	chr17:38338000-38344600	Weak transcription	Brain Anterior Caudate	brain
50	chr17:38338000-38344800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links