Variant report

Variant	rs241955
Chromosome Location	chr19:38278677-38278678
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	chr19:38269925..38271716-chr19:38277161..38278734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000189144	Chromatin interaction
ENSG00000267422	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1056405	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11083428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083430	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11083434	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11665869	0.91[EUR][1000 genomes]
rs11666021	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11666662	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11666738	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs11672257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11672440	1.00[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs11672724	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12162238	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12459013	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12460230	0.90[JPT][hapmap]
rs12460735	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462505	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17249047	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2290999	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs241935	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs241952	0.94[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241954	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35205379	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3848624	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4088299	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356596	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4510143	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60731897	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7248397	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7254809	0.90[EUR][1000 genomes]
rs73025630	0.91[EUR][1000 genomes]
rs73027418	0.90[EUR][1000 genomes]
rs73039018	0.87[ASN][1000 genomes]
rs73041004	0.96[EUR][1000 genomes]
rs73041022	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73041034	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73041045	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73041047	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103383	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8108245	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv960835	chr19:38270238-38293706	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38270800-38279800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:38270800-38281000	Weak transcription	Right Ventricle	heart
3	chr19:38270800-38281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:38271000-38281000	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:38271400-38281000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:38277000-38280600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr19:38278200-38279400	Weak transcription	Pancreas	Pancrea
8	chr19:38278200-38280800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links