Variant report

Variant	rs180405
Chromosome Location	chr12:47164118-47164119
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	TCF12	chr12:47164113-47164766	MCF-7	breast:	n/a	n/a
2	PBX3	chr12:47164112-47165013	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr12:47164094-47164944	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr12:47164036-47165767	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr12:47164049-47165036	SK-N-SH	brain:	n/a	chr12:47164482-47164498 chr12:47164486-47164493 chr12:47164485-47164493 chr12:47164486-47164493 chr12:47164485-47164495 chr12:47164486-47164493 chr12:47164486-47164495
6	TCF12	chr12:47163975-47165772	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr12:47164008-47165768	SK-N-SH	brain:	n/a	chr12:47164482-47164498 chr12:47164486-47164493 chr12:47164485-47164493 chr12:47164486-47164493 chr12:47164485-47164495 chr12:47164486-47164493 chr12:47164486-47164495
8	RXRA	chr12:47164073-47165028	SK-N-SH	brain:	n/a	chr12:47164577-47164584 chr12:47164352-47164366
9	GATA3	chr12:47164088-47164827	MCF-7	breast:	n/a	chr12:47164482-47164498 chr12:47164486-47164493 chr12:47164485-47164493 chr12:47164486-47164493 chr12:47164485-47164495 chr12:47164486-47164493 chr12:47164486-47164495

Variant related genes	Relation type
SLC38A4	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11183581	0.81[EUR][1000 genomes]
rs11183589	0.82[EUR][1000 genomes]
rs11183605	0.87[CEU][hapmap];0.97[GIH][hapmap];0.88[EUR][1000 genomes]
rs11615446	0.82[EUR][1000 genomes]
rs12303637	0.81[EUR][1000 genomes]
rs12307895	0.88[EUR][1000 genomes]
rs12311710	0.88[EUR][1000 genomes]
rs12313822	0.80[EUR][1000 genomes]
rs12316767	0.87[CEU][hapmap]
rs12318216	0.81[EUR][1000 genomes]
rs12320235	0.82[EUR][1000 genomes]
rs12320632	0.81[EUR][1000 genomes]
rs12322157	0.81[EUR][1000 genomes]
rs1468970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180407	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180409	0.87[CHB][hapmap]
rs180410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180412	0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180416	0.87[CHB][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs180417	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180419	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180420	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180421	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180426	0.94[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes]
rs180427	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs180429	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs180430	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2080689	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287471	0.87[CEU][hapmap]
rs2408621	0.82[EUR][1000 genomes]
rs2408623	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2430916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2430920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2430921	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]
rs2465582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs2465584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs2465595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2543334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2543335	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2715783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768136	0.85[EUR][1000 genomes]
rs4768750	0.81[EUR][1000 genomes]
rs4768751	0.80[EUR][1000 genomes]
rs56819961	0.82[EUR][1000 genomes]
rs7316285	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs180405	ADAMTS20	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47149600-47165400	Weak transcription	Pancreas	Pancrea
2	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:47159400-47164200	Strong transcription	Liver	Liver
4	chr12:47160600-47164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:47161800-47165200	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:47163000-47164200	Genic enhancers	HSMM	muscle
8	chr12:47163000-47164200	Enhancers	NHLF	lung
9	chr12:47163000-47165200	Enhancers	HSMMtube	muscle
10	chr12:47163000-47166200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:47163200-47164200	Enhancers	HepG2	liver
12	chr12:47163200-47165200	Weak transcription	Psoas Muscle	Psoas
13	chr12:47163400-47164200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr12:47163400-47164200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:47163400-47164200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr12:47163400-47165200	Enhancers	Fetal Kidney	kidney
17	chr12:47163400-47165400	Enhancers	Fetal Lung	lung
18	chr12:47163400-47167800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr12:47163600-47164200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:47163600-47164200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:47163600-47164200	Enhancers	Osteobl	bone
22	chr12:47163600-47164400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:47163600-47165800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:47163600-47165800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:47163600-47166000	Enhancers	Adipose Nuclei	Adipose
26	chr12:47163600-47167400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:47163600-47168400	Enhancers	Hela-S3	cervix
28	chr12:47163800-47164200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:47163800-47164200	Enhancers	NHDF-Ad	bronchial
30	chr12:47163800-47165000	Enhancers	Fetal Heart	heart
31	chr12:47163800-47166200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:47164000-47164200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:47164000-47165800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:47164000-47165800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links