Variant report

Variant	rs8001432
Chromosome Location	chr13:48576489-48576490
allele	G/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	TFAP2C	chr13:48574861-48576517	Hela-S3	cervix:	n/a	chr13:48575177-48575192
2	TCF7L2	chr13:48575208-48576583	Hela-S3	cervix:	n/a	n/a
3	MAX	chr13:48576175-48576545	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr13:48574590-48576716	IMR90	lung:	n/a	n/a
5	POLR2A	chr13:48576343-48576543	MCF-7	breast:	n/a	n/a
6	POLR2A	chr13:48574745-48576639	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:

Variant related genes	Relation type
SUCLA2	TF binding region
ENSG00000136143	Chromatin interaction
ENSG00000136159	Chromatin interaction

Extended variants
information (count: 152 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1041070	0.89[ASN][1000 genomes]
rs1098354	0.84[ASN][1000 genomes]
rs11148099	0.85[ASN][1000 genomes]
rs11148100	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11618397	0.86[ASN][1000 genomes]
rs1185727	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12864691	0.85[AFR][1000 genomes]
rs1326135	0.91[ASN][1000 genomes]
rs1326136	0.86[ASN][1000 genomes]
rs1326138	0.82[ASN][1000 genomes]
rs1326139	0.82[ASN][1000 genomes]
rs1326140	0.83[ASN][1000 genomes]
rs1536301	0.86[ASN][1000 genomes]
rs1544078	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17071168	0.87[ASN][1000 genomes]
rs1853929	0.82[ASN][1000 genomes]
rs1886975	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1926089	0.86[ASN][1000 genomes]
rs2031590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031591	0.83[AFR][1000 genomes]
rs2094194	0.88[ASN][1000 genomes]
rs2148243	0.89[ASN][1000 genomes]
rs2148244	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2148245	0.86[ASN][1000 genomes]
rs2182376	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2296573	0.84[AFR][1000 genomes]
rs2296574	0.91[ASN][1000 genomes]
rs2406693	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2406697	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2406698	0.88[ASN][1000 genomes]
rs2406699	0.84[ASN][1000 genomes]
rs4245347	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4447314	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4522322	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941621	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942725	0.84[ASN][1000 genomes]
rs4942726	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942727	0.85[ASN][1000 genomes]
rs4942728	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4942729	0.89[ASN][1000 genomes]
rs4942730	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4942735	0.91[ASN][1000 genomes]
rs4942739	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61973260	0.82[EUR][1000 genomes]
rs6561417	0.86[ASN][1000 genomes]
rs6561419	0.89[ASN][1000 genomes]
rs6561420	0.89[ASN][1000 genomes]
rs6561424	0.91[ASN][1000 genomes]
rs6561427	0.90[ASN][1000 genomes]
rs6561430	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6561431	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6561432	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs718010	0.86[ASN][1000 genomes]
rs7318770	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319245	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320366	0.88[ASN][1000 genomes]
rs7320461	0.86[ASN][1000 genomes]
rs7320759	0.86[ASN][1000 genomes]
rs7322515	0.89[ASN][1000 genomes]
rs7325189	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7325437	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7326889	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7326984	0.89[ASN][1000 genomes]
rs7327730	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7328525	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328537	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329419	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7330130	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7330913	0.88[ASN][1000 genomes]
rs7331285	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7332304	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7333659	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7333821	0.86[ASN][1000 genomes]
rs7334207	0.86[ASN][1000 genomes]
rs7335788	0.86[ASN][1000 genomes]
rs7336972	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7337004	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7337744	0.91[ASN][1000 genomes]
rs7338125	0.86[ASN][1000 genomes]
rs7338373	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7338894	0.84[ASN][1000 genomes]
rs765809	0.86[ASN][1000 genomes]
rs7989231	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7990244	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990266	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990505	0.89[ASN][1000 genomes]
rs7994359	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7996580	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7997802	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998116	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7998260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998497	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998998	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7999505	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8000164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001871	0.87[AFR][1000 genomes]
rs9316339	0.88[ASN][1000 genomes]
rs9316343	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316344	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9526417	0.83[ASN][1000 genomes]
rs9526422	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526423	0.86[ASN][1000 genomes]
rs9526426	0.86[ASN][1000 genomes]
rs9526429	0.91[ASN][1000 genomes]
rs9526430	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9526433	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526434	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534876	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9534877	0.86[ASN][1000 genomes]
rs9534878	0.86[ASN][1000 genomes]
rs9534879	0.86[ASN][1000 genomes]
rs9534880	0.86[ASN][1000 genomes]
rs9534882	0.85[ASN][1000 genomes]
rs9534885	0.86[ASN][1000 genomes]
rs9534889	0.89[ASN][1000 genomes]
rs9534892	0.88[ASN][1000 genomes]
rs9534896	0.87[ASN][1000 genomes]
rs9534897	0.83[ASN][1000 genomes]
rs9534898	0.91[ASN][1000 genomes]
rs9534901	0.91[ASN][1000 genomes]
rs9534903	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534904	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9534905	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9534906	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9534907	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534908	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9534909	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9534912	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9534913	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534918	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9534919	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9534922	0.89[ASN][1000 genomes]
rs9534923	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9534926	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9534929	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9562787	0.86[ASN][1000 genomes]
rs9567954	0.89[ASN][1000 genomes]
rs9567955	0.89[ASN][1000 genomes]
rs9567958	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9567959	0.86[ASN][1000 genomes]
rs9567960	0.86[ASN][1000 genomes]
rs9567963	0.86[ASN][1000 genomes]
rs9567964	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9567972	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9567976	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9567979	0.80[AFR][1000 genomes]
rs9567980	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9567986	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9595815	0.88[ASN][1000 genomes]
rs9595825	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8001432	SUCLA2	cis	Muscle Skeletal	GTEx
rs8001432	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48573000-48576600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr13:48574600-48576600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:48574600-48576600	Active TSS	Brain Cingulate Gyrus	brain
4	chr13:48574800-48576600	Active TSS	Brain Anterior Caudate	brain
5	chr13:48574800-48576600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr13:48575000-48576600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:48576000-48576600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:48576000-48576600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:48576000-48576600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr13:48576000-48576600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:48576000-48576600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:48576000-48576600	Enhancers	Colonic Mucosa	Colon
13	chr13:48576000-48576600	Enhancers	Placenta	Placenta
14	chr13:48576000-48576600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr13:48576000-48576600	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr13:48576000-48576600	Active TSS	Stomach Smooth Muscle	stomach
17	chr13:48576000-48576600	Enhancers	HUVEC	blood vessel
18	chr13:48576000-48576600	Enhancers	NHDF-Ad	bronchial
19	chr13:48576000-48576600	Enhancers	NHLF	lung
20	chr13:48576000-48576800	Enhancers	H1 Cell Line	embryonic stem cell
21	chr13:48576000-48576800	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr13:48576000-48576800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:48576000-48576800	Enhancers	Fetal Brain Male	brain
24	chr13:48576000-48576800	Enhancers	HMEC	breast
25	chr13:48576000-48577800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr13:48576000-48578000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr13:48576000-48578200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr13:48576000-48578400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:48576000-48580200	Weak transcription	HSMM	muscle
30	chr13:48576000-48582800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr13:48576000-48583200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:48576000-48583400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr13:48576000-48583600	Weak transcription	HSMMtube	muscle
35	chr13:48576000-48583800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr13:48576000-48587000	Weak transcription	Primary B cells from cord blood	blood
37	chr13:48576000-48587000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:48576000-48588400	Weak transcription	Fetal Intestine Large	intestine
39	chr13:48576000-48589800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr13:48576000-48590800	Weak transcription	Gastric	stomach
41	chr13:48576000-48603600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:48576000-48604000	Weak transcription	Primary T cells from cord blood	blood
43	chr13:48576000-48604800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr13:48576000-48604800	Weak transcription	Fetal Stomach	stomach
45	chr13:48576000-48604800	Weak transcription	Thymus	Thymus
46	chr13:48576000-48610800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr13:48576000-48611400	Weak transcription	Left Ventricle	heart
48	chr13:48576200-48576600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:48576200-48576600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr13:48576200-48576600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links