Variant report

Variant	rs11949390
Chromosome Location	chr5:60558886-60558887
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	chr5:60549933..60553711-chr5:60556075..60559631,4	MCF-7	breast:
2	chr5:60548575..60550984-chr5:60558808..60560811,2	K562	blood:

Variant related genes	Relation type
ENSG00000249279	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10041973	0.93[ASN][1000 genomes]
rs10052753	0.86[AFR][1000 genomes]
rs10056472	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10075959	0.86[AFR][1000 genomes]
rs10076568	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10079115	0.93[ASN][1000 genomes]
rs10939894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11744226	0.81[AFR][1000 genomes]
rs11745696	0.86[AFR][1000 genomes]
rs11747588	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11750566	0.86[AFR][1000 genomes]
rs11960587	0.80[ASN][1000 genomes]
rs12696981	0.93[ASN][1000 genomes]
rs12696982	0.98[ASN][1000 genomes]
rs13156118	0.80[ASN][1000 genomes]
rs13167234	0.90[ASN][1000 genomes]
rs13167244	0.90[ASN][1000 genomes]
rs13167246	0.84[ASN][1000 genomes]
rs13179814	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13181515	0.86[AFR][1000 genomes]
rs13181517	0.86[AFR][1000 genomes]
rs13183007	0.86[AFR][1000 genomes]
rs13186053	0.81[AFR][1000 genomes]
rs13187871	0.88[ASN][1000 genomes]
rs13190305	0.81[AFR][1000 genomes]
rs13355792	0.93[ASN][1000 genomes]
rs28409386	0.81[AFR][1000 genomes]
rs4235485	0.93[ASN][1000 genomes]
rs4315878	0.85[CHB][hapmap];0.98[ASN][1000 genomes]
rs4379148	0.93[ASN][1000 genomes]
rs4640746	0.85[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs4700415	0.90[ASN][1000 genomes]
rs62366231	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62366234	0.83[ASN][1000 genomes]
rs6449523	0.86[CHB][hapmap];0.98[ASN][1000 genomes]
rs67749311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72759289	0.88[ASN][1000 genomes]
rs72759299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72761408	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7721603	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9291707	1.00[YRI][hapmap]

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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60556000-60570200	Weak transcription	HSMM	muscle
3	chr5:60557800-60559600	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:60558000-60566400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:60558200-60559400	Weak transcription	Stomach Mucosa	stomach
6	chr5:60558200-60559400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:60558200-60559600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:60558200-60559600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:60558200-60559600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:60558200-60559600	Enhancers	Brain Anterior Caudate	brain
11	chr5:60558200-60559600	Weak transcription	Right Atrium	heart
12	chr5:60558200-60560600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:60558400-60559400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:60558600-60559400	Enhancers	HUVEC	blood vessel
15	chr5:60558600-60560000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:60558800-60559600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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