Variant report

Variant	rs4668380
Chromosome Location	chr2:172128676-172128677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172128253..172130254-chr2:172289100..172291873,2	MCF-7	breast:
2	chr2:172126634..172129658-chr2:172132451..172134211,3	MCF-7	breast:
3	chr2:172124703..172126558-chr2:172126623..172128823,2	MCF-7	breast:
4	chr2:172015584..172019101-chr2:172128501..172131090,3	MCF-7	breast:
5	chr2:172123232..172126602-chr2:172127090..172129825,3	K562	blood:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11691073	0.88[CEU][hapmap]
rs11694321	0.89[CEU][hapmap]
rs13003130	0.82[CEU][hapmap]
rs13023973	0.89[CEU][hapmap]
rs13031794	0.89[CEU][hapmap]
rs1477180	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1811271	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1987418	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2111459	0.89[CEU][hapmap]
rs888273	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9653289	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4668380	PPIG	cis	parietal	SCAN
rs4668380	CDCA7	cis	cerebellum	SCAN
rs4668380	HAT1	cis	parietal	SCAN
rs4668380	DDX6	trans	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172126800-172128800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr2:172127000-172129000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:172127400-172129800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:172127600-172128800	Enhancers	Fetal Brain Male	brain
5	chr2:172127600-172129000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:172127600-172129000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:172127600-172129000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:172127600-172129200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:172127600-172130000	Enhancers	HMEC	breast
10	chr2:172127600-172130400	Enhancers	Colon Smooth Muscle	Colon
11	chr2:172127800-172128800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:172127800-172129000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:172127800-172129000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:172127800-172129000	Enhancers	NHDF-Ad	bronchial
15	chr2:172127800-172129200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:172127800-172129200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:172127800-172129200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:172127800-172129200	Flanking Active TSS	A549	lung
19	chr2:172127800-172129800	Enhancers	Hela-S3	cervix
20	chr2:172127800-172134000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:172128000-172128800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:172128000-172128800	Enhancers	Aorta	Aorta
23	chr2:172128000-172129000	Enhancers	Rectal Smooth Muscle	rectum
24	chr2:172128000-172129000	Enhancers	NH-A	brain
25	chr2:172128000-172129200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:172128000-172129200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:172128000-172129200	Enhancers	Fetal Stomach	stomach
28	chr2:172128000-172129200	Enhancers	Osteobl	bone
29	chr2:172128000-172130000	Enhancers	Stomach Smooth Muscle	stomach
30	chr2:172128200-172128800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:172128200-172128800	Enhancers	Fetal Brain Female	brain
32	chr2:172128200-172129000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr2:172128200-172129000	Enhancers	HepG2	liver
34	chr2:172128200-172129000	Enhancers	HSMM	muscle
35	chr2:172128200-172129000	Enhancers	HUVEC	blood vessel
36	chr2:172128400-172128800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:172128400-172129000	Enhancers	NHLF	lung
38	chr2:172128400-172129200	Enhancers	Placenta	Placenta
39	chr2:172128600-172128800	Flanking Bivalent TSS/Enh	K562	blood
40	chr2:172128600-172128800	Enhancers	NHEK	skin
41	chr2:172128600-172129000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:172128600-172129000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:172128600-172129400	Enhancers	Pancreas	Pancrea
44	chr2:172128600-172134200	Weak transcription	HSMMtube	muscle

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