Variant report

Variant	rs6427631
Chromosome Location	chr1:154370020-154370021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154367430..154370038-chr1:154375786..154377764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1073907	0.82[AMR][1000 genomes]
rs10908834	0.82[EUR][1000 genomes]
rs10908835	0.94[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs11265606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265609	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577266	0.82[AMR][1000 genomes]
rs11580178	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11582424	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11585004	0.83[ASN][1000 genomes]
rs12127600	0.94[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.80[ASN][1000 genomes]
rs1889314	0.82[EUR][1000 genomes]
rs1889315	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34437053	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56211693	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6427627	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs6659828	0.81[AMR][1000 genomes]
rs6661909	0.81[EUR][1000 genomes]
rs6698130	0.81[AMR][1000 genomes]
rs7525436	0.81[EUR][1000 genomes]
rs952146	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs9651054	0.85[ASN][1000 genomes]
rs9662562	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9724691	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6427631	TARS2	cis	parietal	SCAN
rs6427631	SHC1	cis	parietal	SCAN
rs6427631	SLC39A1	cis	cerebellum	SCAN
rs6427631	S100A5	cis	parietal	SCAN
rs6427631	GATAD2B	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154364400-154377200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:154367200-154374200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:154370000-154370800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:154370000-154371000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:154370000-154371400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr1:154370000-154371600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr1:154370000-154377200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links