Variant report

Variant	rs4660956
Chromosome Location	chr1:47158486-47158487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47153374..47156939-chr1:47157123..47159935,3	K562	blood:
2	chr1:47148439..47150795-chr1:47155891..47158836,3	K562	blood:
3	chr1:47156029..47159013-chr1:47175919..47177585,2	K562	blood:
4	chr1:47157744..47160542-chr1:47181134..47183864,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10749863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749864	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211337	0.87[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];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[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];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545206	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595898	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1816730	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1866770	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890473	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083485	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099766	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2218191	0.94[EUR][1000 genomes]
rs2476158	0.92[EUR][1000 genomes]
rs35050319	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861275	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097354	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553120	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]
rs4660359	0.84[ASN][1000 genomes]
rs601060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618505	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668899	0.84[ASN][1000 genomes]
rs7516616	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4660956	EFCAB14	cis	Whole Blood	GTEx
rs4660956	ATPAF1	cis	multi-tissue	Pritchard
rs4660956	EFCAB14	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
2	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
5	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
7	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:47142000-47159400	Strong transcription	K562	blood
12	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:47142600-47159200	Strong transcription	GM12878-XiMat	blood
14	chr1:47142600-47159400	Strong transcription	NHEK	skin
15	chr1:47142800-47158800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:47142800-47159600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:47142800-47159800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:47143200-47159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:47143200-47159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:47143200-47159800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr1:47143600-47159400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:47143800-47159400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:47143800-47159400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:47143800-47159800	Strong transcription	Primary T cells from cord blood	blood
25	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:47144600-47159600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:47145400-47159000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:47145800-47158800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:47148400-47159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:47148800-47159400	Strong transcription	Hela-S3	cervix
31	chr1:47152200-47158800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:47153000-47159000	Strong transcription	Spleen	Spleen
33	chr1:47153200-47159400	Genic enhancers	Fetal Thymus	thymus
34	chr1:47153400-47159600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:47153600-47159400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:47153600-47159600	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:47153800-47158800	Strong transcription	Lung	lung
38	chr1:47154000-47158600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:47154000-47159400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:47154000-47159400	Strong transcription	Liver	Liver
41	chr1:47154000-47159800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:47154000-47159800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:47154000-47161000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:47154600-47159200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:47155400-47158800	Genic enhancers	Thymus	Thymus
47	chr1:47155600-47161000	Weak transcription	Fetal Brain Male	brain
48	chr1:47155600-47169000	Weak transcription	Stomach Mucosa	stomach
49	chr1:47155800-47158600	Weak transcription	Psoas Muscle	Psoas
50	chr1:47155800-47158800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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