Variant report

Variant	rs6822794
Chromosome Location	chr4:78157822-78157823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78155142..78157870-chr4:78168469..78170209,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10005142	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10009384	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.82[ASN][1000 genomes]
rs10010290	0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10018359	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10020351	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10025838	0.91[JPT][hapmap]
rs10026129	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10026795	0.83[ASN][1000 genomes]
rs10030735	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10030867	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10030957	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs1006042	0.91[JPT][hapmap]
rs10856957	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097729	0.81[ASN][1000 genomes]
rs11097730	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.82[ASN][1000 genomes]
rs11097741	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12504397	0.81[ASN][1000 genomes]
rs12508219	0.83[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12509168	0.91[JPT][hapmap]
rs12640093	0.91[JPT][hapmap]
rs1477314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1559119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1968235	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28503908	0.81[CEU][hapmap]
rs4280759	0.91[JPT][hapmap]
rs4285107	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4504280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4536958	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4538513	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4547817	0.91[JPT][hapmap]
rs4563522	0.89[JPT][hapmap]
rs4576030	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4582179	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4582180	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4859475	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859751	0.84[CEU][hapmap]
rs4859752	0.96[CEU][hapmap]
rs4859753	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859754	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859755	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859756	0.91[JPT][hapmap]
rs4859758	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6532904	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6532919	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532921	0.96[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6838744	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840915	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs6844009	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845599	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs6846698	0.91[JPT][hapmap]
rs6857792	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs7690427	0.92[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1011551	chr4:78120872-78204224	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1012298	chr4:78120872-78255427	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv997743	chr4:78126462-78217004	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1014055	chr4:78132200-78255427	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013602	chr4:78133566-78217004	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1007726	chr4:78133566-78255427	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1001852	chr4:78135874-78260269	ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1013302	chr4:78136251-78192318	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv998972	chr4:78139780-78240303	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1010406	chr4:78139780-78255427	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1014305	chr4:78139780-78260269	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1003755	chr4:78145279-78255427	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1014450	chr4:78157527-78255427	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6822794	BMP3	cis	parietal	SCAN
rs6822794	CCNG2	cis	cerebellum	SCAN
rs6822794	CXCL9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78157800-78165400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links