Variant report

Variant	rs4512020
Chromosome Location	chr4:79859212-79859213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79471198..79473938-chr4:79857809..79860687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138772	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10018189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10023100	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10028067	0.94[CEU][hapmap]
rs10034295	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10857059	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs11722437	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1275045	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1275046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1275047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1299129	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs13108247	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480718	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871706	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs1979444	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046104	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2288254	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2554395	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3937772	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]
rs62308043	0.90[ASN][1000 genomes]
rs6534083	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534086	1.00[ASN][1000 genomes]
rs6534087	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534090	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6846743	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6854347	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656083	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664339	0.90[MEX][hapmap]
rs7664587	0.94[CEU][hapmap];0.90[MEX][hapmap]
rs7677084	0.84[MEX][hapmap]
rs7688534	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9307446	0.94[CEU][hapmap]
rs931149	0.82[ASN][1000 genomes]
rs931150	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9993426	0.82[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	nsv879504	chr4:79759796-79874275	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4512020	ANXA3	cis	multi-tissue	Pritchard
rs4512020	LIN54	cis	cerebellum	SCAN
rs4512020	NAAA	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79794200-79859600	Weak transcription	Colonic Mucosa	Colon
2	chr4:79814600-79859600	Weak transcription	Fetal Kidney	kidney
3	chr4:79833000-79859800	Weak transcription	Esophagus	oesophagus
4	chr4:79833000-79859800	Weak transcription	Right Ventricle	heart
5	chr4:79833200-79859600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:79833600-79859800	Weak transcription	Placenta	Placenta
7	chr4:79845800-79860000	Weak transcription	Small Intestine	intestine
8	chr4:79849200-79859600	Weak transcription	Fetal Lung	lung
9	chr4:79850600-79859600	Weak transcription	HSMMtube	muscle
10	chr4:79850800-79859400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:79850800-79859400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:79850800-79859400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:79850800-79859600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:79850800-79859600	Weak transcription	Ovary	ovary
15	chr4:79850800-79859800	Weak transcription	Left Ventricle	heart
16	chr4:79850800-79859800	Weak transcription	Pancreas	Pancrea
17	chr4:79850800-79860000	Weak transcription	Gastric	stomach
18	chr4:79850800-79860000	Weak transcription	Lung	lung
19	chr4:79850800-79860000	Weak transcription	Spleen	Spleen
20	chr4:79851400-79859600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:79851600-79859400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:79851800-79859600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:79854000-79859800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:79854200-79859400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:79854400-79859400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:79855000-79859600	Weak transcription	Fetal Thymus	thymus
27	chr4:79857000-79859600	Weak transcription	Liver	Liver
28	chr4:79857800-79859600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:79858000-79859600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:79858000-79859600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr4:79858000-79859600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:79858000-79859600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:79858000-79859600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr4:79858000-79859600	Enhancers	Colon Smooth Muscle	Colon
35	chr4:79858000-79859600	Enhancers	HepG2	liver
36	chr4:79858000-79859800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:79858000-79859800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr4:79858200-79859400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr4:79858200-79859400	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr4:79858400-79859600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr4:79858400-79859600	Enhancers	Psoas Muscle	Psoas
42	chr4:79858600-79859400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:79858600-79859400	Enhancers	Primary T cells from cord blood	blood
44	chr4:79858600-79859600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr4:79858600-79859800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr4:79858600-79860000	Flanking Active TSS	Dnd41	blood
47	chr4:79858800-79859400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:79858800-79859400	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr4:79858800-79859600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr4:79858800-79859600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links