Variant report

Variant	rs2397212
Chromosome Location	chr6:56143231-56143232
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	TEAD4	chr6:56142947-56143354	H1-hESC	embryonic stem cell:	n/a	n/a
2	JUND	chr6:56142946-56143249	A549	lung:	n/a	n/a
3	POLR2A	chr6:56142773-56143592	SK-N-MC	brain:	n/a	n/a
4	EP300	chr6:56142828-56143422	A549	lung:	n/a	n/a
5	SP1	chr6:56142735-56143351	A549	lung:	n/a	n/a
6	GATA3	chr6:56142830-56143498	A549	lung:	n/a	chr6:56143355-56143365 chr6:56142832-56142842
7	REST	chr6:56142808-56143344	A549	lung:	n/a	n/a
8	TCF12	chr6:56142639-56143411	A549	lung:	n/a	n/a
9	FOSL2	chr6:56142846-56143337	A549	lung:	n/a	n/a
10	BCL3	chr6:56142843-56143422	A549	lung:	n/a	n/a
11	FOXA2	chr6:56142833-56143384	A549	lung:	n/a	n/a
12	FOXP2	chr6:56142775-56143298	SK-N-MC	brain:	n/a	n/a
13	FOXA2	chr6:56142810-56143366	A549	lung:	n/a	n/a
14	EP300	chr6:56142656-56143340	A549	lung:	n/a	n/a
15	SP1	chr6:56142725-56143401	A549	lung:	n/a	n/a
16	GATA3	chr6:56142902-56143408	A549	lung:	n/a	chr6:56143355-56143365

Variant related genes	Relation type
ENSG00000219095	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10498810	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.80[ASN][1000 genomes]
rs10948981	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12530020	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12665485	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1925158	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925160	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925163	0.82[CHD][hapmap]
rs1925187	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925188	0.81[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap];0.82[ASN][1000 genomes]
rs2328693	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2397210	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2397213	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807013	0.83[JPT][hapmap]
rs3846927	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846928	0.80[ASN][1000 genomes]
rs3846929	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846931	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4119562	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4119563	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712121	0.81[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4715602	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715603	0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55734123	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66796842	0.84[ASN][1000 genomes]
rs67454631	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72645374	0.84[ASN][1000 genomes]
rs7745111	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759570	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349807	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9349809	0.81[ASN][1000 genomes]
rs9370495	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382597	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382598	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9382599	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9382601	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382603	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382604	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396185	0.81[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs994039	0.82[JPT][hapmap]
rs994040	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2397212	COL21A1	cis	cerebellum	SCAN
rs2397212	KLHL31	cis	parietal	SCAN
rs2397212	TRAM2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56141000-56143400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:56142000-56144000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:56142400-56143800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr6:56142600-56145000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:56142800-56143600	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:56142800-56143600	Enhancers	Fetal Lung	lung
7	chr6:56142800-56143800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:56142800-56144400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:56142800-56144600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr6:56142800-56144800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:56143000-56143400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:56143000-56143400	Enhancers	Fetal Muscle Leg	muscle
13	chr6:56143000-56143600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:56143000-56143800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:56143000-56143800	Enhancers	Fetal Stomach	stomach
16	chr6:56143000-56144000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr6:56143000-56144000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:56143200-56143400	Flanking Active TSS	A549	lung

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