Variant report

Variant	rs4553120
Chromosome Location	chr1:47165729-47165730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:47165177-47165740	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47163880..47168035-chr1:47177746..47180775,3	K562	blood:

Variant related genes	Relation type
EFCAB14	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10749863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473292	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1545206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595898	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1816730	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1866770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890473	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099766	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165317	1.00[YRI][hapmap]
rs2218191	0.94[EUR][1000 genomes]
rs2476158	0.92[EUR][1000 genomes]
rs35050319	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861275	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097354	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660359	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4660954	1.00[YRI][hapmap]
rs4660956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618505	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668899	0.84[ASN][1000 genomes]
rs7516616	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893954	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4553120	EFCAB14	cis	Esophagus Mucosa	GTEx
rs4553120	EFCAB14	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47155600-47169000	Weak transcription	Stomach Mucosa	stomach
5	chr1:47157600-47172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:47158200-47172000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:47158800-47171000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:47159400-47171200	Weak transcription	Right Ventricle	heart
10	chr1:47159400-47172200	Weak transcription	Psoas Muscle	Psoas
11	chr1:47159600-47168200	Weak transcription	HMEC	breast
12	chr1:47160600-47165800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:47160600-47169000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:47160600-47169400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:47160600-47173600	Strong transcription	Primary T cells from cord blood	blood
16	chr1:47160600-47174000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:47160600-47181200	Strong transcription	Dnd41	blood
18	chr1:47160800-47166000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:47160800-47166000	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:47160800-47166000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:47160800-47166200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:47160800-47166600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:47160800-47168600	Strong transcription	Left Ventricle	heart
24	chr1:47160800-47174000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:47160800-47175400	Strong transcription	Liver	Liver
26	chr1:47160800-47181800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:47160800-47182200	Strong transcription	Primary B cells from cord blood	blood
28	chr1:47160800-47182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:47160800-47182400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:47160800-47182600	Strong transcription	Placenta	Placenta
31	chr1:47161000-47165800	Strong transcription	K562	blood
32	chr1:47161000-47173400	Strong transcription	Primary hematopoietic stem cells	blood
33	chr1:47161000-47173800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:47161200-47182200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:47161400-47182200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:47161400-47182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:47161600-47167000	Weak transcription	Gastric	stomach
38	chr1:47161600-47168000	Weak transcription	Pancreas	Pancrea
39	chr1:47161600-47170800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:47161800-47169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:47161800-47170600	Weak transcription	Fetal Intestine Small	intestine
42	chr1:47162000-47166600	Weak transcription	Colonic Mucosa	Colon
43	chr1:47162000-47169800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:47162200-47167000	Weak transcription	HUVEC	blood vessel
45	chr1:47162200-47167200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:47162200-47168200	Weak transcription	Fetal Heart	heart
47	chr1:47162200-47170000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:47162200-47170200	Weak transcription	Small Intestine	intestine
49	chr1:47162400-47166800	Weak transcription	Brain Germinal Matrix	brain
50	chr1:47162400-47166800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links