Variant report

Variant	rs4557129
Chromosome Location	chr3:111456859-111456860
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111456141..111458585-chr3:111526075..111527610,2	MCF-7	breast:
2	chr3:111452923..111457246-chr3:111577346..111581538,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10804492	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711582	0.81[CHD][hapmap]
rs11922220	0.90[CEU][hapmap]
rs12490337	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs12495513	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12632878	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325897	0.90[CEU][hapmap]
rs4491869	0.81[CEU][hapmap]
rs4682299	0.81[CHD][hapmap]
rs4682302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438003	0.81[CHD][hapmap]
rs6782962	0.85[CEU][hapmap]
rs6784441	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs6788543	0.81[CHD][hapmap]
rs6796087	0.81[CHD][hapmap]
rs6801225	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629156	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs955382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4557129	SAT2	trans	parietal	SCAN
rs4557129	CD200	cis	cerebellum	SCAN
rs4557129	POMZP3	trans	lymphoblastoid	seeQTL
rs4557129	GAP43	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111452400-111458800	Enhancers	HMEC	breast
4	chr3:111452600-111457200	Enhancers	HSMM	muscle
5	chr3:111452800-111459200	Enhancers	Osteobl	bone
6	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:111453400-111458600	Enhancers	HSMMtube	muscle
9	chr3:111453600-111458800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:111453600-111458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
12	chr3:111453800-111457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:111453800-111457600	Enhancers	NHEK	skin
14	chr3:111454200-111458200	Enhancers	Hela-S3	cervix
15	chr3:111454600-111458000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:111454600-111459400	Enhancers	HepG2	liver
17	chr3:111454600-111459600	Enhancers	Liver	Liver
18	chr3:111454800-111460400	Enhancers	Fetal Heart	heart
19	chr3:111454800-111464400	Weak transcription	Placenta	Placenta
20	chr3:111455000-111457600	Weak transcription	HUVEC	blood vessel
21	chr3:111455000-111461000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr3:111455200-111457000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:111455600-111457000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:111455600-111458600	Enhancers	Right Atrium	heart
25	chr3:111455600-111458800	Enhancers	Adipose Nuclei	Adipose
26	chr3:111455800-111457000	Enhancers	Small Intestine	intestine
27	chr3:111455800-111457200	Enhancers	Fetal Stomach	stomach
28	chr3:111455800-111458400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:111455800-111458400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:111455800-111458600	Enhancers	Psoas Muscle	Psoas
31	chr3:111455800-111458800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:111455800-111459000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:111455800-111459200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:111455800-111461000	Enhancers	Rectal Smooth Muscle	rectum
35	chr3:111456000-111457000	Enhancers	Fetal Thymus	thymus
36	chr3:111456000-111457600	Enhancers	Fetal Lung	lung
37	chr3:111456000-111458200	Enhancers	Colon Smooth Muscle	Colon
38	chr3:111456000-111458600	Enhancers	Stomach Smooth Muscle	stomach
39	chr3:111456000-111458800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:111456000-111459000	Enhancers	Fetal Muscle Leg	muscle
41	chr3:111456000-111459000	Enhancers	Stomach Mucosa	stomach
42	chr3:111456200-111457200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:111456200-111457400	Enhancers	Fetal Kidney	kidney
44	chr3:111456200-111459000	Flanking Active TSS	A549	lung
45	chr3:111456200-111465600	Weak transcription	Primary T cells from cord blood	blood
46	chr3:111456400-111457200	Enhancers	GM12878-XiMat	blood
47	chr3:111456400-111457600	Weak transcription	Left Ventricle	heart
48	chr3:111456400-111457600	Weak transcription	Ovary	ovary
49	chr3:111456400-111457600	Weak transcription	Pancreas	Pancrea
50	chr3:111456400-111457600	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links