Variant report

Variant	rs13384181
Chromosome Location	chr2:234775346-234775347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234765045..234768392-chr2:234769046..234775688,6	K562	blood:
2	chr2:234773117..234776003-chr2:234811783..234814431,2	K562	blood:
3	chr2:234766693..234769626-chr2:234773837..234776124,2	MCF-7	breast:
4	2:234635414-234639782..2:234772667-234780240	Hela-S3	cervix:
5	2:234683624-234705119..2:234772667-234780240	Hela-S3	cervix:
6	2:234772667-234780240..2:234954947-234965240	Hela-S3	cervix:
7	2:234543708-234558325..2:234772667-234780240	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000241635	Chromatin interaction
ENSG00000185038	Chromatin interaction
ENSG00000072080	Chromatin interaction
ENSG00000234143	Chromatin interaction
ENSG00000243135	Chromatin interaction
ENSG00000242515	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10164928	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185631	0.88[MEX][hapmap];0.83[TSI][hapmap]
rs10204079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390675	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13399418	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862931	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17863803	1.00[CHD][hapmap]
rs17864768	1.00[YRI][hapmap]
rs6431637	1.00[AFR][1000 genomes]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13384181	FGD5	trans	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234763600-234776800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:234763800-234775400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:234763800-234776600	Weak transcription	Right Ventricle	heart
4	chr2:234764000-234776400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:234764000-234776600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:234764000-234776600	Weak transcription	HUVEC	blood vessel
7	chr2:234764200-234776600	Weak transcription	Primary B cells from cord blood	blood
8	chr2:234764200-234776600	Weak transcription	Primary T cells from cord blood	blood
9	chr2:234764200-234776600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:234764200-234776600	Weak transcription	HMEC	breast
11	chr2:234764200-234776600	Weak transcription	NH-A	brain
12	chr2:234764200-234776600	Weak transcription	NHDF-Ad	bronchial
13	chr2:234764200-234776600	Weak transcription	NHEK	skin
14	chr2:234764200-234776800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:234764400-234776400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:234764400-234776600	Weak transcription	HSMM	muscle
17	chr2:234767000-234776600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:234771200-234776800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:234773000-234776000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:234773800-234776600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:234774200-234775800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:234774200-234775800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:234774200-234776600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:234774400-234775600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:234774400-234775800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:234774400-234775800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr2:234774400-234775800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:234774400-234775800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:234774400-234775800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:234774400-234776000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:234774400-234776000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:234774400-234776000	ZNF genes & repeats	A549	lung
33	chr2:234774400-234776200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:234774600-234776000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:234774600-234776800	ZNF genes & repeats	Placenta	Placenta
36	chr2:234774800-234775800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:234774800-234775800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:234774800-234775800	ZNF genes & repeats	Liver	Liver
39	chr2:234774800-234776000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:234774800-234776000	Strong transcription	Osteobl	bone
41	chr2:234775000-234775400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:234775000-234775600	Strong transcription	NHLF	lung
43	chr2:234775000-234775800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:234775000-234775800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:234775000-234775800	ZNF genes & repeats	K562	blood
46	chr2:234775000-234776000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:234775000-234776400	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr2:234775000-234776600	Weak transcription	Fetal Lung	lung
49	chr2:234775000-234776800	ZNF genes & repeats	Fetal Stomach	stomach
50	chr2:234775200-234775400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links