Variant report

Variant	rs2024562
Chromosome Location	chr6:69451081-69451082
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:69450619..69452838-chr6:69487007..69488538,2	K562	blood:
2	chr6:69449624..69452933-chr6:69485444..69489658,4	K562	blood:
3	chr6:69343299..69346561-chr6:69450371..69455015,5	K562	blood:
4	chr6:69449408..69453188-chr6:69468664..69472430,3	K562	blood:
5	chr6:69444346..69447984-chr6:69448039..69451471,5	K562	blood:
6	chr6:69438284..69440310-chr6:69450555..69453510,2	K562	blood:
7	chr6:69426489..69429415-chr6:69449508..69452167,3	K562	blood:

Variant related genes	Relation type
ENSG00000230910	Chromatin interaction
ENSG00000135298	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10945140	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs1357618	0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1357619	0.83[JPT][hapmap]
rs1403927	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1523937	0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs1523947	0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs1523948	0.85[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs1983623	0.95[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2064389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2140510	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2177448	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2204285	0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2206834	1.00[JPT][hapmap]
rs2206836	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223724	0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2257875	0.83[EUR][1000 genomes]
rs2585601	0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs2585603	0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2746128	0.95[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2746133	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs4708243	0.83[JPT][hapmap]
rs562010	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.98[ASN][1000 genomes]
rs6455295	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6455296	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6455298	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6455302	1.00[JPT][hapmap]
rs6455303	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6911395	0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6920537	0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs6928142	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6929378	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6932940	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7738291	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7739996	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7743793	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746943	0.93[GIH][hapmap]
rs7747313	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747314	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754795	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755356	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7769724	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9294806	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9294807	1.00[JPT][hapmap]
rs9294810	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs9294811	1.00[JPT][hapmap]
rs9346239	1.00[JPT][hapmap]
rs9346240	0.86[CHD][hapmap];0.92[JPT][hapmap]
rs9346243	1.00[JPT][hapmap]
rs9346245	1.00[JPT][hapmap]
rs9346246	0.81[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs9354796	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9360357	0.83[JPT][hapmap]
rs9360361	0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs9363961	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9363963	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9446057	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9446058	1.00[JPT][hapmap]
rs9454611	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9454616	0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs9454621	0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs9454622	1.00[JPT][hapmap]
rs992784	0.92[JPT][hapmap]

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	nsv886130	chr6:68950298-69531957	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2024562	BAI3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69440800-69456800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:69440800-69456800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:69444800-69457000	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:69448400-69452200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:69449000-69451800	Weak transcription	Brain Angular Gyrus	brain
6	chr6:69449800-69453000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:69450000-69452200	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:69450200-69451600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:69450200-69451600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:69450200-69452200	Enhancers	Primary T cells from cord blood	blood
11	chr6:69450400-69451600	Flanking Active TSS	K562	blood
12	chr6:69450600-69451200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:69450600-69451600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:69450600-69451800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:69450600-69452000	Enhancers	Fetal Lung	lung
16	chr6:69450800-69451200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:69451000-69451600	Enhancers	Primary monocytes fromperipheralblood	blood

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