Variant report

Variant	rs1853956
Chromosome Location	chr1:153444509-153444510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153327328..153331635-chr1:153443588..153448842,6	MCF-7	breast:
2	chr1:153443878..153448578-chr1:153449187..153452566,7	MCF-7	breast:
3	chr1:153331254..153333129-chr1:153443301..153445517,2	MCF-7	breast:
4	chr1:153442375..153445170-chr1:153456426..153458929,2	MCF-7	breast:
5	chr1:153443002..153445359-chr1:153445547..153447150,2	K562	blood:
6	chr1:153336539..153339701-chr1:153443875..153445928,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1359627	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409367	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1409368	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1555886	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835341	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16835343	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1998844	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2026563	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2339694	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2986206	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2986210	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2986214	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006426	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3006428	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3006429	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3006430	0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3006433	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3006438	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3014829	0.82[ASN][1000 genomes]
rs3014831	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3014832	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3014833	0.84[ASN][1000 genomes]
rs3014835	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3014836	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3014838	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3014839	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3014843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3014849	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3014851	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3125233	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587742	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6667320	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs719081	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875501	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9435988	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9633411	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153441000-153447400	Weak transcription	Fetal Heart	heart
2	chr1:153444000-153447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links