Variant report

Variant	rs4859567
Chromosome Location	chr4:76852839-76852840
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76848097..76850409-chr4:76852802..76854673,2	MCF-7	breast:
2	chr4:76846485..76850652-chr4:76851327..76855093,5	K562	blood:
3	chr4:76850798..76854400-chr4:76859062..76863095,5	MCF-7	breast:
4	chr4:76852145..76854131-chr4:76857580..76859399,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138744	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs10007919	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs10009947	0.82[EUR][1000 genomes]
rs10021434	0.84[CEU][hapmap]
rs10031733	1.00[CEU][hapmap]
rs10031983	0.82[CEU][hapmap]
rs10518143	0.88[CEU][hapmap]
rs12374321	1.00[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12374370	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13105416	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111494	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs13118503	0.94[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs13129896	0.82[EUR][1000 genomes]
rs13130917	0.82[CEU][hapmap]
rs17001247	1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1857821	1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2242470	0.94[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2271528	0.94[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2276886	0.94[CEU][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs28375800	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28422144	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28451731	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28532601	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28535831	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28588114	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28595360	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28647886	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2869462	0.88[CEU][hapmap]
rs34630680	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3733233	0.89[ASN][1000 genomes]
rs3733234	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs3733235	0.89[ASN][1000 genomes]
rs3733238	1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs3796484	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4859568	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859569	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859570	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859571	1.00[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859572	0.89[CEU][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859573	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859578	0.93[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4859580	0.94[CEU][hapmap]
rs4859609	0.90[MEX][hapmap]
rs56148877	0.94[ASN][1000 genomes]
rs56300358	0.94[ASN][1000 genomes]
rs6824911	0.91[ASN][1000 genomes]
rs6841837	0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs6847815	1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs71594936	0.92[ASN][1000 genomes]
rs7670521	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[ASN][1000 genomes]
rs884004	0.88[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs9994667	0.82[CEU][hapmap];0.90[MEX][hapmap]
rs9996608	0.94[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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS 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	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4859567	NAAA	cis	Adipose Subcutaneous	GTEx
rs4859567	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs4859567	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs4859567	NAAA	cis	Muscle Skeletal	GTEx
rs4859567	NAAA	cis	Whole Blood	GTEx
rs4859567	FAM47E	cis	cerebellum	SCAN
rs4859567	NAAA	cis	parietal	SCAN
rs4859567	ASAHL	cis	multi-tissue	Pritchard
rs4859567	CDKL2	cis	parietal	SCAN
rs4859567	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs4859567	NAAA	cis	Esophagus Muscularis	GTEx
rs4859567	NAAA	cis	Esophagus Mucosa	GTEx
rs4859567	NAAA	cis	lymphoblastoid	seeQTL
rs4859567	NAAA	cis	Artery Aorta	GTEx
rs4859567	CXCL11	cis	multi-tissue	Pritchard
rs4859567	NAAA	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76832600-76859000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:76833800-76856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:76833800-76860800	Weak transcription	Fetal Heart	heart
4	chr4:76835000-76859400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:76835000-76859600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:76835200-76859800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:76837000-76857200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:76837000-76860200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:76837200-76860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:76837200-76860800	Weak transcription	HSMM	muscle
11	chr4:76837600-76858400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:76837600-76859200	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:76837600-76860800	Weak transcription	Fetal Kidney	kidney
14	chr4:76837800-76860800	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:76837800-76860800	Weak transcription	NH-A	brain
16	chr4:76838000-76857600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:76838600-76860800	Weak transcription	NHLF	lung
18	chr4:76839000-76860400	Weak transcription	HUVEC	blood vessel
19	chr4:76839400-76860800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:76839600-76859200	Weak transcription	Brain Substantia Nigra	brain
21	chr4:76839800-76860800	Weak transcription	Psoas Muscle	Psoas
22	chr4:76839800-76860800	Weak transcription	HMEC	breast
23	chr4:76841800-76857400	Weak transcription	Osteobl	bone
24	chr4:76841800-76860800	Weak transcription	Brain Germinal Matrix	brain
25	chr4:76842000-76855800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:76842000-76857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:76842000-76860400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:76842400-76860800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:76842600-76860800	Weak transcription	Pancreas	Pancrea
30	chr4:76843000-76860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:76843000-76860800	Weak transcription	Thymus	Thymus
32	chr4:76843000-76860800	Weak transcription	NHEK	skin
33	chr4:76843400-76859800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:76843400-76860000	Weak transcription	A549	lung
35	chr4:76843400-76861000	Weak transcription	Small Intestine	intestine
36	chr4:76845400-76860800	Weak transcription	Right Ventricle	heart
37	chr4:76845600-76860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:76846000-76857000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:76846000-76860800	Weak transcription	HSMMtube	muscle
40	chr4:76846400-76855800	Strong transcription	Fetal Intestine Small	intestine
41	chr4:76847200-76855800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:76848800-76855800	Strong transcription	Liver	Liver
43	chr4:76849000-76853800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:76849200-76853000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr4:76849200-76853200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:76849200-76853200	Strong transcription	Left Ventricle	heart
47	chr4:76849200-76853400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:76849200-76854000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:76849200-76854400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:76849200-76858000	Strong transcription	Primary T cells fromperipheralblood	blood

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