Variant report

Variant	rs17035289
Chromosome Location	chr4:106048291-106048292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:105884034..105895590-chr4:106044778..106053207,47	MCF-7	breast:
2	chr4:105932463..105936165-chr4:106047602..106049768,3	MCF-7	breast:
3	chr4:105816771..105820576-chr4:106045760..106049308,12	MCF-7	breast:
4	chr4:106041526..106043206-chr4:106047664..106049788,2	MCF-7	breast:
5	chr4:105982359..105982999-chr4:106047359..106048436,4	MCF-7	breast:
6	chr4:105886561..105894585-chr4:106043962..106052941,18	MCF-7	breast:
7	chr4:105826232..105829985-chr4:106045106..106049151,6	MCF-7	breast:
8	chr4:105412086..105414232-chr4:106046630..106049413,2	MCF-7	breast:
9	chr4:105976784..105986292-chr4:106044571..106052702,25	MCF-7	breast:
10	chr4:106046108..106050165-chr4:106391446..106394724,4	MCF-7	breast:
11	chr4:106048208..106050465-chr4:106092982..106095215,2	MCF-7	breast:
12	chr4:105813669..105816273-chr4:106047766..106049998,5	MCF-7	breast:
13	chr4:105816661..105820025-chr4:106046680..106052012,4	MCF-7	breast:
14	chr4:105980136..105985353-chr4:106046016..106051646,9	MCF-7	breast:
15	chr4:105804976..105807566-chr4:106046221..106048902,2	MCF-7	breast:
16	chr4:106037748..106040803-chr4:106047611..106051482,3	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000248373	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000168772	Chromatin interaction
ENSG00000245384	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10488913	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11097881	0.82[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11729069	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17035311	1.00[ASW][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17616993	0.88[ASN][1000 genomes]
rs6843555	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17035289	BDH2	cis	cerebellum	SCAN
rs17035289	PPP3CA	cis	cerebellum	SCAN
rs17035289	TET2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106047400-106048600	Enhancers	Fetal Lung	lung
2	chr4:106047800-106048400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:106048200-106050400	Weak transcription	Fetal Heart	heart

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Input of quick search could be:

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

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