Variant report

Variant	rs7972522
Chromosome Location	chr12:50421257-50421258
allele	A/G
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	USF1	chr12:50421113-50421389	ECC-1	luminal epithelium:	n/a	chr12:50421277-50421288
2	USF1	chr12:50421171-50421377	HepG2	liver:	n/a	chr12:50421277-50421288
3	USF1	chr12:50421146-50421371	H1-hESC	embryonic stem cell:	n/a	chr12:50421277-50421288
4	USF1	chr12:50421148-50421366	HepG2	liver:	n/a	chr12:50421277-50421288
5	USF1	chr12:50420954-50421393	HCT-116	colon:	n/a	chr12:50421277-50421288
6	USF1	chr12:50421112-50421366	ECC-1	luminal epithelium:	n/a	chr12:50421277-50421288
7	USF2	chr12:50421224-50421417	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50420531..50422273-chr12:50423775..50426347,2	K562	blood:
2	chr12:50419178..50421274-chr12:50425998..50428027,2	MCF-7	breast:
3	chr12:50024399..50026763-chr12:50420346..50422300,2	MCF-7	breast:
4	chr12:50419454..50422134-chr12:50422205..50423893,2	MCF-7	breast:
5	chr12:50419603..50421266-chr12:50430358..50432423,2	K562	blood:

Variant related genes	Relation type
RACGAP1	TF binding region
ENSG00000161800	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10161020	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[EUR][1000 genomes]
rs10161120	0.98[EUR][1000 genomes]
rs10875992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs11169232	0.86[EUR][1000 genomes]
rs11169234	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11169247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169256	1.00[EUR][1000 genomes]
rs11169259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169260	0.98[EUR][1000 genomes]
rs11835014	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11836389	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12298110	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12311010	0.96[EUR][1000 genomes]
rs12317586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17124264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs2291612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs2292720	1.00[EUR][1000 genomes]
rs378943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4297542	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55634523	0.96[EUR][1000 genomes]
rs55652312	0.94[EUR][1000 genomes]
rs55802497	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55936104	0.98[EUR][1000 genomes]
rs55990533	0.98[EUR][1000 genomes]
rs56099252	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56159935	1.00[EUR][1000 genomes]
rs56232366	0.94[EUR][1000 genomes]
rs56259551	1.00[EUR][1000 genomes]
rs57014171	1.00[EUR][1000 genomes]
rs57045365	0.94[EUR][1000 genomes]
rs60000653	1.00[EUR][1000 genomes]
rs60042968	1.00[EUR][1000 genomes]
rs60456498	1.00[EUR][1000 genomes]
rs60905953	1.00[EUR][1000 genomes]
rs611434	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs661823	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs694851	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7131715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7306035	0.96[EUR][1000 genomes]
rs7308994	1.00[EUR][1000 genomes]
rs7309480	1.00[EUR][1000 genomes]
rs7309940	1.00[EUR][1000 genomes]
rs7309966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73119648	0.82[EUR][1000 genomes]
rs73119651	1.00[EUR][1000 genomes]
rs73119660	1.00[EUR][1000 genomes]
rs73119664	1.00[EUR][1000 genomes]
rs73119671	1.00[EUR][1000 genomes]
rs73119681	0.98[EUR][1000 genomes]
rs73119688	0.98[EUR][1000 genomes]
rs73119690	0.98[EUR][1000 genomes]
rs7961683	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7979958	1.00[EUR][1000 genomes]
rs9325146	1.00[EUR][1000 genomes]
rs9669608	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50419400-50426600	Weak transcription	Gastric	stomach
2	chr12:50419800-50421400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:50419800-50426400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:50420000-50424000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:50420000-50426000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:50420000-50426200	Weak transcription	Primary B cells from cord blood	blood
7	chr12:50420200-50426200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:50420200-50426200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:50420200-50426400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:50421000-50422400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr12:50421200-50421800	Enhancers	HepG2	liver

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