Variant report

Variant	rs2576970
Chromosome Location	chr12:104278787-104278788
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	RAD21	chr12:104277613-104278976	SK-N-SH	brain:	n/a	n/a
2	YY1	chr12:104278787-104279128	GM12892	blood:	n/a	chr12:104278965-104278977
3	YY1	chr12:104278741-104279054	GM12891	blood:	n/a	chr12:104278965-104278977
4	CTCF	chr12:104278740-104278890	AG04450	lung:	n/a	n/a
5	CTCF	chr12:104277847-104278936	A549	lung:	n/a	chr12:104278381-104278394 chr12:104278195-104278211
6	CTCF	chr12:104278640-104278790	HPF	lung:	n/a	n/a
7	MXI1	chr12:104277868-104279101	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104233142..104235484-chr12:104276450..104278828,3	K562	blood:
2	chr12:104276117..104279238-chr12:104322705..104326968,4	K562	blood:
3	chr12:104277824..104279928-chr12:104282058..104285020,2	K562	blood:
4	chr12:104277028..104280742-chr12:104283520..104285730,3	K562	blood:
5	chr12:104262529..104265193-chr12:104278298..104280290,2	K562	blood:
6	chr12:104276555..104279337-chr12:104325468..104328815,4	K562	blood:
7	chr12:104233142..104235198-chr12:104276474..104278828,2	K562	blood:

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000257327	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000111696	Chromatin interaction
ENSG00000166598	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1000295	0.91[JPT][hapmap]
rs10745982	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10745983	0.85[YRI][hapmap]
rs10745987	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10745988	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10778293	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs10778298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10778300	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10778301	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10861128	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10861129	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10861134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10861137	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10861138	0.86[JPT][hapmap]
rs10861139	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs11111817	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs11111820	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs11111822	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11612613	0.91[MEX][hapmap]
rs1165596	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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]
rs1165597	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1165598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11830285	0.88[YRI][hapmap]
rs1185985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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]
rs12312978	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1595338	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[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]
rs1595339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2118313	0.91[JPT][hapmap]
rs2196614	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2248382	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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]
rs2251979	0.88[CEU][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap]
rs2252000	0.88[CEU][hapmap]
rs2374351	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2374353	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2576957	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2576961	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[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]
rs2576962	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2576963	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2576964	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2583236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2583241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2583242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2583243	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2583245	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2583246	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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]
rs2583247	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2583248	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2888809	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2888810	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs3850016	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs3850017	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs3850019	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4491322	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4556622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[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]
rs4590949	0.88[YRI][hapmap]
rs4964118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136272	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7136297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7138145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7138345	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs728165	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs728166	0.84[CHD][hapmap];0.91[JPT][hapmap]
rs7295268	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7295499	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7298655	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7299349	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7301439	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7310988	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7311473	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7314790	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7964654	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs878125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9943761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9943762	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9943844	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9988931	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv977145	chr12:104273790-104283207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv3420727	chr12:104278729-104278879	Enhancers Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2576970	GNN	cis	parietal	SCAN
rs2576970	SLC5A8	cis	parietal	SCAN
rs2576970	NFYB	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104275000-104281600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr12:104276800-104278800	Enhancers	GM12878-XiMat	blood
3	chr12:104278200-104279200	Enhancers	Thymus	Thymus
4	chr12:104278200-104285800	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links