Variant report

Variant	rs17049299
Chromosome Location	chr2:58241734-58241735
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58241265..58242265-chr8:43096231..43096912,2	MCF-7	breast:
2	chr2:58240285..58243265-chr8:43094257..43096723,2	K562	blood:
3	chr2:58240418..58242396-chr2:58273310..58275258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10188390	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10210198	0.87[ASN][1000 genomes]
rs10496084	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10496085	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs10496086	0.82[CEU][hapmap]
rs10496087	0.82[CEU][hapmap]
rs11898024	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12463540	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12470403	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12470851	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12471043	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12473840	0.82[CEU][hapmap]
rs12476222	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12478718	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1371212	0.82[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1401101	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1518396	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1518397	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1518398	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1518403	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1607378	0.80[EUR][1000 genomes]
rs17049282	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17049288	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17049308	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17049312	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17049314	0.82[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17049316	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17049321	0.80[EUR][1000 genomes]
rs17049394	0.82[CEU][hapmap]
rs17830749	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs34191187	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34821621	0.81[EUR][1000 genomes]
rs35876471	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3771203	0.83[EUR][1000 genomes]
rs55723561	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55856965	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56136700	0.81[EUR][1000 genomes]
rs56370078	0.83[EUR][1000 genomes]
rs58995859	0.82[EUR][1000 genomes]
rs59309072	0.86[ASN][1000 genomes]
rs61548822	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545679	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6719889	0.81[ASN][1000 genomes]
rs6732965	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67484511	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6755324	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs67880350	0.81[EUR][1000 genomes]
rs67919965	0.81[EUR][1000 genomes]
rs72808488	0.82[EUR][1000 genomes]
rs72808489	0.82[EUR][1000 genomes]
rs72808491	0.82[EUR][1000 genomes]
rs72808498	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72808501	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72810305	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72810306	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72810307	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72810308	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72810316	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72810317	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72810318	0.81[ASN][1000 genomes]
rs72810320	0.83[EUR][1000 genomes]
rs72810323	0.81[EUR][1000 genomes]
rs72810325	0.81[EUR][1000 genomes]
rs728574	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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