Variant report

Variant	rs7303531
Chromosome Location	chr12:50420003-50420004
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	FOXM1	chr12:50418755-50420034	ECC-1	luminal epithelium:	n/a	n/a
2	MXI1	chr12:50418042-50420024	IMR90	lung:	n/a	n/a
3	GABPA	chr12:50418950-50420117	A549	lung:	n/a	chr12:50419376-50419387 chr12:50419376-50419390
4	YY1	chr12:50418844-50420032	SK-N-SH	brain:	n/a	chr12:50419489-50419511 chr12:50419249-50419263 chr12:50419413-50419421 chr12:50419410-50419432 chr12:50419409-50419421 chr12:50419410-50419420
5	GABPA	chr12:50418823-50420167	MCF-7	breast:	n/a	chr12:50419376-50419387 chr12:50419376-50419390
6	POLR2A	chr12:50418653-50420029	GM12891	blood:	n/a	n/a
7	MXI1	chr12:50418130-50420027	SK-N-SH	brain:	n/a	n/a
8	HCFC1	chr12:50417933-50420286	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50358386..50360982-chr12:50417949..50420523,2	MCF-7	breast:
2	chr12:50417982..50420791-chr12:50450221..50452010,2	MCF-7	breast:
3	chr12:50235029..50238212-chr12:50416884..50420841,4	K562	blood:
4	chr12:50410558..50416843-chr12:50417238..50421054,9	MCF-7	breast:
5	chr12:50419178..50421274-chr12:50425998..50428027,2	MCF-7	breast:
6	chr12:50359827..50361683-chr12:50418817..50420770,2	MCF-7	breast:
7	chr12:50419417..50420920-chr12:50438136..50440896,2	K562	blood:
8	chr12:50418073..50421025-chr12:50559963..50562659,2	MCF-7	breast:
9	chr12:50419454..50422134-chr12:50422205..50423893,2	MCF-7	breast:
10	chr12:50419603..50421266-chr12:50430358..50432423,2	K562	blood:

Variant related genes	Relation type
RACGAP1	TF binding region
ENSG00000110881	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000086159	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10161020	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10161120	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875990	0.90[GIH][hapmap]
rs10875992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs10875993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169232	0.86[EUR][1000 genomes]
rs11169234	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169247	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11169256	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169259	0.98[EUR][1000 genomes]
rs11169260	0.98[EUR][1000 genomes]
rs11835014	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11836389	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298110	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12311010	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12317586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124264	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292720	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307082	0.86[JPT][hapmap]
rs378943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs4297542	1.00[EUR][1000 genomes]
rs55634523	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55652312	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55802497	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55936104	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55990533	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56099252	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56159935	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56232366	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56259551	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57014171	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57045365	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60000653	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60042968	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60456498	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60905953	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611434	0.94[EUR][1000 genomes]
rs615382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs629754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs661823	0.83[EUR][1000 genomes]
rs694851	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs7131715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306035	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7308994	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309480	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7309940	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7309966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119648	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73119651	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73119660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119681	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73119688	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73119690	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7961683	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7979958	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9325146	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669608	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50419400-50426600	Weak transcription	Gastric	stomach
2	chr12:50419800-50420200	Enhancers	Primary hematopoietic stem cells	blood
3	chr12:50419800-50420200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr12:50419800-50420200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr12:50419800-50420200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:50419800-50421000	Weak transcription	A549	lung
7	chr12:50419800-50421200	Weak transcription	HepG2	liver
8	chr12:50419800-50421400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:50419800-50426400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:50420000-50420200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:50420000-50420200	Enhancers	Dnd41	blood
12	chr12:50420000-50421000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:50420000-50424000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:50420000-50426000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:50420000-50426200	Weak transcription	Primary B cells from cord blood	blood

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