Variant report

Variant	rs6449523
Chromosome Location	chr5:60561748-60561749
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60456708..60458931-chr5:60559806..60562109,2	MCF-7	breast:
2	chr5:60560892..60563443-chr5:60571695..60574490,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10041973	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10056472	0.95[ASN][1000 genomes]
rs10079115	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939894	0.98[ASN][1000 genomes]
rs10939895	1.00[ASN][1000 genomes]
rs11747588	0.95[ASN][1000 genomes]
rs11949390	0.86[CHB][hapmap];0.98[ASN][1000 genomes]
rs11960587	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12189420	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12696981	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12696982	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156118	0.82[ASN][1000 genomes]
rs13167234	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13167244	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13167246	0.86[ASN][1000 genomes]
rs13179814	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13187871	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13355792	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4235485	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4315878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379148	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4640746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700415	0.93[ASN][1000 genomes]
rs62366231	0.95[ASN][1000 genomes]
rs62366234	0.86[ASN][1000 genomes]
rs67749311	0.95[ASN][1000 genomes]
rs72759289	0.90[ASN][1000 genomes]
rs72759299	1.00[ASN][1000 genomes]
rs72761408	0.90[ASN][1000 genomes]
rs7721603	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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:17 , 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	chr5:60558000-60566400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:60559400-60562000	Enhancers	Stomach Mucosa	stomach
5	chr5:60560000-60569200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:60560400-60562000	Enhancers	HUVEC	blood vessel
7	chr5:60560400-60569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:60560600-60564400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:60560600-60564400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:60560600-60564400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:60560600-60569000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:60560800-60561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:60560800-60563000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:60560800-60571200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:60561000-60563800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr5:60561000-60569000	Weak transcription	Brain Substantia Nigra	brain
17	chr5:60561000-60573200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links