Variant report

Variant	rs4955414
Chromosome Location	chr3:49317727-49317728
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49313590..49315716-chr3:49315985..49318300,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188315	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10154992	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	1.00[ASN][1000 genomes]
rs11130183	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130186	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130187	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130190	1.00[ASN][1000 genomes]
rs11710434	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720542	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720657	1.00[ASN][1000 genomes]
rs12583	1.00[ASN][1000 genomes]
rs12637346	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13084037	1.00[ASN][1000 genomes]
rs13322887	1.00[ASN][1000 genomes]
rs2082923	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099526	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs3448	1.00[ASN][1000 genomes]
rs35713889	1.00[ASN][1000 genomes]
rs4384984	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4955417	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4955421	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955423	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955427	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955430	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4955439	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955443	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259943	1.00[ASN][1000 genomes]
rs62259944	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs6446256	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446257	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6769821	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778080	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785045	1.00[ASN][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6808036	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809204	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809851	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7429661	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7617480	1.00[ASN][1000 genomes]
rs7619016	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626076	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631586	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9586	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9831648	1.00[ASN][1000 genomes]
rs9834003	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842132	1.00[ASN][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9860285	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9867285	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871024	1.00[ASN][1000 genomes]
rs9881860	0.82[EUR][1000 genomes];1.00[ASN][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	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4955414	NICN1-AS1	cis	Thyroid	GTEx
rs4955414	PFKFB4	cis	Nerve Tibial	GTEx
rs4955414	WDR6	cis	Muscle Skeletal	GTEx
rs4955414	AMT	cis	Thyroid	GTEx
rs4955414	AMT	cis	Artery Tibial	GTEx
rs4955414	WDR6	cis	Heart Left Ventricle	GTEx
rs4955414	AMT	cis	Nerve Tibial	GTEx
rs4955414	AMT	cis	Artery Aorta	GTEx
rs4955414	AMT	cis	Whole Blood	GTEx
rs4955414	AMT	cis	Esophagus Mucosa	GTEx
rs4955414	NICN1	cis	Thyroid	GTEx
rs4955414	WDR6	cis	Nerve Tibial	GTEx
rs4955414	AMT	cis	Muscle Skeletal	GTEx
rs4955414	AMT	cis	Adipose Subcutaneous	GTEx
rs4955414	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4955414	AMT	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49313200-49318600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:49313200-49326200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49313200-49349400	Strong transcription	Dnd41	blood
5	chr3:49313400-49318600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:49314200-49324200	Strong transcription	Hela-S3	cervix
8	chr3:49314800-49318000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:49314800-49318600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:49314800-49318800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:49314800-49320800	Weak transcription	Fetal Brain Male	brain
12	chr3:49314800-49321000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:49314800-49321000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:49314800-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:49315000-49318800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:49315000-49318800	Strong transcription	Thymus	Thymus
19	chr3:49315000-49320800	Weak transcription	Aorta	Aorta
20	chr3:49315000-49320800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:49315000-49321000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:49315200-49318400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:49315200-49318400	Strong transcription	Primary B cells from cord blood	blood
24	chr3:49315200-49318400	Strong transcription	Brain Germinal Matrix	brain
25	chr3:49315200-49318400	Strong transcription	K562	blood
26	chr3:49315200-49318600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:49315200-49318600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:49315200-49318800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:49315200-49319200	Strong transcription	Lung	lung
30	chr3:49315200-49320800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:49315200-49320800	Weak transcription	Psoas Muscle	Psoas
32	chr3:49315200-49321000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:49315200-49327600	Strong transcription	Placenta	Placenta
34	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
39	chr3:49315400-49317800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:49315400-49318000	Weak transcription	Colonic Mucosa	Colon
41	chr3:49315400-49318400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:49315400-49318400	Strong transcription	Primary T cells from cord blood	blood
43	chr3:49315400-49318400	Strong transcription	NH-A	brain
44	chr3:49315400-49318600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:49315400-49318800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:49315400-49320800	Weak transcription	Fetal Heart	heart
47	chr3:49315400-49320800	Weak transcription	Small Intestine	intestine
48	chr3:49315400-49321000	Weak transcription	Stomach Mucosa	stomach
49	chr3:49315400-49321000	Weak transcription	A549	lung
50	chr3:49315400-49327600	Strong transcription	GM12878-XiMat	blood

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