Variant report

Variant	rs7637889
Chromosome Location	chr3:134026087-134026088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:
2	chr3:134026032..134027592-chr3:134187039..134189717,2	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:
4	chr3:134025588..134027447-chr3:134198814..134200765,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214289	Chromatin interaction
ENSG00000114019	Chromatin interaction
ENSG00000260633	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10935116	1.00[CHB][hapmap]
rs11917363	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11919447	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11923513	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11928672	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs11928742	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11928907	0.85[EUR][1000 genomes]
rs12487438	1.00[CHB][hapmap]
rs13069766	0.81[EUR][1000 genomes]
rs13071132	1.00[CHB][hapmap]
rs13084853	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13085145	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090504	0.85[EUR][1000 genomes]
rs13097926	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1498730	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17312996	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17313003	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs34006849	0.82[EUR][1000 genomes]
rs34549392	0.81[EUR][1000 genomes]
rs35527623	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35558600	0.82[EUR][1000 genomes]
rs35878592	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4234421	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339087	1.00[CHB][hapmap]
rs5002434	0.85[EUR][1000 genomes]
rs5002435	0.84[EUR][1000 genomes]
rs5002436	0.84[EUR][1000 genomes]
rs5002437	0.84[EUR][1000 genomes]
rs55682444	0.81[EUR][1000 genomes]
rs56019901	0.81[EUR][1000 genomes]
rs6439474	1.00[CHB][hapmap]
rs6768709	1.00[CHB][hapmap]
rs6772791	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs6809909	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs71331753	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71331755	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7609766	0.81[EUR][1000 genomes]
rs7613323	0.81[EUR][1000 genomes]
rs7613440	0.80[EUR][1000 genomes]
rs7613450	0.81[EUR][1000 genomes]
rs7614069	0.81[EUR][1000 genomes]
rs7636249	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7638751	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7639784	1.00[ASN][1000 genomes]
rs7642519	0.81[EUR][1000 genomes]
rs7647682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647778	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs9826364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827007	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7637889	CCRL1	cis	cerebellum	SCAN
rs7637889	TMEM22	cis	parietal	SCAN
rs7637889	CA5A	trans	parietal	SCAN
rs7637889	CEP70	cis	cerebellum	SCAN
rs7637889	PPP2R3A	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134015800-134026800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:134018400-134026800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:134018600-134026800	Weak transcription	A549	lung
4	chr3:134018600-134027000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:134019000-134026800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:134020600-134026800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:134022400-134027000	Weak transcription	Fetal Lung	lung
8	chr3:134023800-134032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:134025200-134031600	Weak transcription	Ovary	ovary
10	chr3:134025600-134030800	Weak transcription	Spleen	Spleen
11	chr3:134026000-134028600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:134026000-134029200	Enhancers	HMEC	breast

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