Variant report

Variant	rs17035227
Chromosome Location	chr4:105984033-105984034
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75976428..75978953-chr4:105982186..105984226,2	MCF-7	breast:
2	chr4:105980136..105985353-chr4:106046016..106051646,9	MCF-7	breast:
3	chr4:105982631..105985650-chr4:105987239..105989362,4	MCF-7	breast:
4	chr4:105976784..105986292-chr4:106044571..106052702,25	MCF-7	breast:
5	chr4:105975764..105988950-chr4:106062358..106070647,39	MCF-7	breast:
6	chr4:105812011..105813887-chr4:105981924..105984058,2	MCF-7	breast:
7	chr4:105982064..105984157-chr4:105988059..105990663,2	MCF-7	breast:
8	chr4:105817670..105820970-chr4:105982686..105984664,5	MCF-7	breast:
9	chr4:105982346..105984231-chr4:106059044..106061638,2	MCF-7	breast:
10	chr4:105976101..105984516-chr4:106064112..106070622,19	MCF-7	breast:
11	chr4:105982559..105986858-chr4:106036992..106040333,4	MCF-7	breast:
12	chr4:105829249..105833469-chr4:105980777..105984054,6	MCF-7	breast:
13	chr4:105887583..105897108-chr4:105977318..105984912,20	MCF-7	breast:
14	chr4:105981696..105984518-chr4:105989745..105992068,2	MCF-7	breast:
15	chr4:105982372..105984745-chr4:106040097..106042240,2	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000251906	Chromatin interaction
ENSG00000248242	Chromatin interaction
ENSG00000248373	Chromatin interaction
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10010512	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10015876	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11728350	1.00[CHD][hapmap]
rs12710978	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13116642	1.00[EUR][1000 genomes]
rs13127473	1.00[CHD][hapmap]
rs17253672	1.00[CHD][hapmap]
rs28763330	0.95[EUR][1000 genomes]
rs28789413	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28821280	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34463758	0.98[EUR][1000 genomes]
rs34887792	0.96[EUR][1000 genomes]
rs66530760	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6811026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6823769	0.98[EUR][1000 genomes]
rs6825684	1.00[CHD][hapmap]
rs6837188	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs763480	1.00[CHD][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	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	nsv830024	chr4:105884350-106037816	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17035227	CXXC4	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:105983000-105984800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:105983000-105985000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:105983200-105985000	Enhancers	GM12878-XiMat	blood
4	chr4:105983200-105985200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:105983600-105989600	Weak transcription	Primary B cells from cord blood	blood
6	chr4:105983800-105984200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr4:105984000-105985000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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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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