Variant report

Variant	rs12022550
Chromosome Location	chr1:153452931-153452932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153451807..153454321-chr1:153580520..153582698,2	MCF-7	breast:
2	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
3	chr1:153444815..153448277-chr1:153449752..153453118,4	MCF-7	breast:
4	chr1:153445670..153449598-chr1:153450178..153453743,4	K562	blood:
5	chr1:153452726..153455263-chr1:153460858..153463511,2	MCF-7	breast:
6	chr1:153449114..153453479-chr1:153459428..153463150,4	MCF-7	breast:
7	chr1:153450588..153453299-chr1:153453645..153457534,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188643	Chromatin interaction
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10888560	0.88[CHB][hapmap];0.82[YRI][hapmap]
rs11205297	0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12021612	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12025638	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036701	0.88[CHB][hapmap]
rs12043280	0.89[JPT][hapmap]
rs12043556	0.89[CHB][hapmap];0.90[YRI][hapmap]
rs12044034	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12047203	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12217109	0.88[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap]
rs16835308	0.88[CHB][hapmap]
rs16835332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696717	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2986209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006414	0.88[CHB][hapmap]
rs3006423	0.88[CHB][hapmap]
rs3014814	0.88[CHB][hapmap]
rs3014818	0.88[CHB][hapmap]
rs3014822	0.88[CHB][hapmap]
rs3014823	0.88[CHB][hapmap]
rs3014848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845348	0.88[CHB][hapmap]
rs55703007	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56009204	0.89[ASN][1000 genomes]
rs72708789	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153450600-153453800	Enhancers	HepG2	liver
2	chr1:153451000-153467400	Weak transcription	Ovary	ovary
3	chr1:153451600-153456200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:153451600-153456200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:153451600-153456400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:153451800-153456200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:153451800-153456400	Weak transcription	Fetal Heart	heart
8	chr1:153452000-153453400	Weak transcription	Esophagus	oesophagus
9	chr1:153452000-153456200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:153452000-153456200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:153452000-153456200	Weak transcription	Fetal Intestine Large	intestine

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