Variant report

Variant	rs2309801
Chromosome Location	chr2:101039956-101039957
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	chr2:101039873-101040743	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:101029935..101035569-chr2:101035669..101041059,9	MCF-7	breast:
2	chr2:101032643..101036022-chr2:101036491..101040981,5	K562	blood:
3	chr2:100907128..100908845-chr2:101037649..101040314,2	MCF-7	breast:
4	chr2:100882939..100884943-chr2:101037829..101040208,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238029	TF binding region
ENSG00000115526	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10167159	0.87[AMR][1000 genomes]
rs10172841	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs10176978	0.88[ASN][1000 genomes]
rs10180570	0.84[AMR][1000 genomes]
rs10180685	0.95[ASN][1000 genomes]
rs10183063	1.00[ASN][1000 genomes]
rs10193535	0.96[GIH][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs10198898	0.85[CHD][hapmap]
rs10206374	0.93[GIH][hapmap]
rs1057056	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1057063	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1057064	1.00[CHB][hapmap]
rs1124009	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13400841	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];1.00[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]
rs1347721	0.90[AMR][1000 genomes]
rs1370627	0.96[GIH][hapmap]
rs1437972	1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[ASN][1000 genomes]
rs1465829	0.85[CHD][hapmap]
rs17024034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17024035	0.96[GIH][hapmap]
rs17024129	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs17024133	0.86[GIH][hapmap]
rs17024136	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs17024144	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs17024203	0.85[CHD][hapmap]
rs17024207	0.85[CHD][hapmap]
rs17024209	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1898573	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2083148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3748934	0.85[CHD][hapmap]
rs3748936	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3791358	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs4149506	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4149509	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4149514	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4149515	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4149516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4149522	0.85[CHD][hapmap]
rs4850932	0.88[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap];0.95[ASN][1000 genomes]
rs55932868	0.88[ASN][1000 genomes]
rs56656536	0.87[AMR][1000 genomes]
rs56741959	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57862179	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58164864	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58674788	0.88[ASN][1000 genomes]
rs59701896	0.88[ASN][1000 genomes]
rs59858985	0.88[ASN][1000 genomes]
rs60468180	0.95[ASN][1000 genomes]
rs60566188	0.88[ASN][1000 genomes]
rs60609848	0.87[AMR][1000 genomes]
rs61710328	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6542933	0.88[ASN][1000 genomes]
rs6542945	0.88[ASN][1000 genomes]
rs6542946	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs6542950	0.85[CHD][hapmap]
rs6706707	0.88[ASN][1000 genomes]
rs6716367	0.87[AMR][1000 genomes]
rs6725672	1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6728575	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs6732285	0.90[GIH][hapmap]
rs6736938	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738454	0.85[CHD][hapmap]
rs6738566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6739589	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6749572	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6750040	1.00[CHB][hapmap]
rs6751629	0.85[CHD][hapmap]
rs6754869	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6755285	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6758622	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6761084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73966105	0.88[ASN][1000 genomes]
rs73966106	0.88[ASN][1000 genomes]
rs73968413	0.88[ASN][1000 genomes]
rs7559084	0.88[ASN][1000 genomes]
rs7561065	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7562184	0.88[ASN][1000 genomes]
rs7562636	0.88[ASN][1000 genomes]
rs7562754	0.88[ASN][1000 genomes]
rs7564178	0.81[AMR][1000 genomes]
rs7565502	0.88[ASN][1000 genomes]
rs7567130	0.90[ASN][1000 genomes]
rs7571410	0.88[ASN][1000 genomes]
rs7571651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7571659	0.94[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.95[ASN][1000 genomes]
rs7575422	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7582096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585898	0.96[GIH][hapmap];0.86[MEX][hapmap]
rs7587333	0.90[AMR][1000 genomes]
rs7596483	0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7598205	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs7598227	0.88[ASN][1000 genomes]
rs7605834	0.88[ASN][1000 genomes]
rs876439	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs9308834	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv582532	chr2:101029002-101531943	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1011990	chr2:101039956-101105648	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101034600-101043000	Weak transcription	Placenta	Placenta
2	chr2:101034800-101043800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:101035000-101040000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:101035200-101040400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:101038800-101040000	Enhancers	Colon Smooth Muscle	Colon
6	chr2:101039400-101040000	Weak transcription	Fetal Lung	lung
7	chr2:101039600-101041000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr2:101039600-101041000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:101039800-101041200	Enhancers	NHDF-Ad	bronchial

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