Variant report

Variant	rs4727774
Chromosome Location	chr7:112117358-112117359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:112116592-112118819	IMR90	lung:	n/a	n/a
2	POLR2A	chr7:112117259-112117731	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:112117232-112117709	GM12891	blood:	n/a	n/a
4	POLR2A	chr7:112117227-112117406	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:112117277-112117450	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:112116143-112117387	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr7:112116027-112120055	A549	lung:	n/a	n/a
8	POLR2A	chr7:112116222-112117766	GM12892	blood:	n/a	n/a
9	POLR2A	chr7:112116196-112117756	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:112115869-112121327	K562	blood:	n/a	n/a
11	POLR2A	chr7:112115373-112119161	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:112116323-112117757	GM12892	blood:	n/a	n/a
13	POLR2A	chr7:112117177-112117718	GM12892	blood:	n/a	n/a
14	POLR2A	chr7:112116155-112118266	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr7:112115993-112117792	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:112116268-112117594	GM12891	blood:	n/a	n/a
17	POLR2A	chr7:112116203-112117829	GM12892	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
2	chr7:112116935..112118572-chr7:112119944..112122258,2	MCF-7	breast:
3	chr7:112108291..112109853-chr7:112116761..112118478,2	MCF-7	breast:
4	chr7:112113016..112114522-chr7:112116589..112118218,2	K562	blood:
5	chr7:112114725..112118373-chr7:112118548..112121134,7	K562	blood:
6	chr7:112109911..112112772-chr7:112114561..112118551,4	K562	blood:

No data

Variant related genes	Relation type
LSMEM1	TF binding region
ENSG00000181016	Chromatin interaction
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1005659	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1005661	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024568	1.00[ASN][1000 genomes]
rs1024569	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024570	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1024571	0.80[AMR][1000 genomes]
rs1024572	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260414	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029631	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500007	0.91[ASN][1000 genomes]
rs1054043	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953712	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953713	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11514940	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764489	0.85[ASN][1000 genomes]
rs11769604	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12154294	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531101	0.86[ASN][1000 genomes]
rs12531636	0.86[ASN][1000 genomes]
rs12539263	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468457	1.00[ASN][1000 genomes]
rs1468458	1.00[ASN][1000 genomes]
rs17159684	0.95[ASN][1000 genomes]
rs17159686	1.00[ASN][1000 genomes]
rs1963308	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041066	0.85[AMR][1000 genomes]
rs2041067	0.86[AMR][1000 genomes]
rs2190587	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396541	0.99[ASN][1000 genomes]
rs2396542	1.00[ASN][1000 genomes]
rs3095035	1.00[ASN][1000 genomes]
rs34633971	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36095669	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807206	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807210	1.00[ASN][1000 genomes]
rs3807213	1.00[ASN][1000 genomes]
rs4275157	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4727771	0.91[ASN][1000 genomes]
rs4730548	0.91[ASN][1000 genomes]
rs4730549	0.91[ASN][1000 genomes]
rs55954386	0.92[ASN][1000 genomes]
rs56020731	0.91[ASN][1000 genomes]
rs6944364	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6945176	0.92[ASN][1000 genomes]
rs6967593	0.92[ASN][1000 genomes]
rs6967894	0.92[ASN][1000 genomes]
rs6968084	0.92[ASN][1000 genomes]
rs6973615	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73201469	1.00[ASN][1000 genomes]
rs7455170	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777925	1.00[ASN][1000 genomes]
rs7817	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4727774	IFRD1	cis	Thyroid	GTEx
rs4727774	IFRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:112094400-112118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:112095200-112117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:112095600-112117400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:112095600-112117400	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:112095600-112117400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr7:112095600-112118800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:112095800-112117400	Strong transcription	Fetal Thymus	thymus
11	chr7:112095800-112118000	Strong transcription	Placenta	Placenta
12	chr7:112095800-112118200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:112095800-112118200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:112096400-112121600	Strong transcription	Liver	Liver
15	chr7:112096400-112121800	Weak transcription	Stomach Mucosa	stomach
16	chr7:112096800-112117600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr7:112100600-112135000	Weak transcription	Esophagus	oesophagus
18	chr7:112101000-112118000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr7:112102400-112117400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:112102600-112117800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:112102800-112119800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:112103000-112117400	Strong transcription	Adipose Nuclei	Adipose
23	chr7:112103000-112117800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr7:112103000-112118200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:112103000-112118200	Strong transcription	Hela-S3	cervix
26	chr7:112103000-112119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr7:112103200-112117600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:112103200-112118200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:112103200-112118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:112103200-112118600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:112103600-112121200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:112103600-112121800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr7:112104600-112118000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:112105600-112121800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr7:112106200-112117400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr7:112107600-112117400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:112107600-112118200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:112107800-112120800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr7:112108200-112117400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:112109800-112118000	Strong transcription	NHLF	lung
41	chr7:112110600-112120400	Weak transcription	Fetal Heart	heart
42	chr7:112110600-112124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:112111200-112127200	Weak transcription	Fetal Brain Male	brain
44	chr7:112111600-112122200	Weak transcription	Fetal Kidney	kidney
45	chr7:112112000-112120400	Weak transcription	Gastric	stomach
46	chr7:112112400-112119400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:112112400-112121800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr7:112112400-112122200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:112112600-112117400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:112112600-112129000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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