Variant report

Variant	rs17616060
Chromosome Location	chr2:142266462-142266463
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:142265321..142267918-chr2:142664161..142666622,2	MCF-7	breast:
2	chr2:142261934..142264280-chr2:142265309..142267485,3	MCF-7	breast:
3	chr2:142259654..142261746-chr2:142265611..142267711,3	MCF-7	breast:
4	chr2:142263240..142267352-chr2:142886657..142889435,3	MCF-7	breast:
5	chr2:142248367..142251172-chr2:142262537..142266743,4	MCF-7	breast:
6	chr2:142223533..142226548-chr2:142266133..142269163,3	MCF-7	breast:
7	chr2:142241833..142244486-chr2:142265674..142268047,2	MCF-7	breast:
8	chr2:142265220..142267079-chr2:142275773..142278354,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10496884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674506	1.00[CEU][hapmap]
rs11675776	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11685267	1.00[CEU][hapmap]
rs11690880	1.00[ASN][1000 genomes]
rs11695833	0.84[EUR][1000 genomes]
rs12992656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12993733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993821	1.00[CEU][hapmap]
rs12994255	0.84[EUR][1000 genomes]
rs13001306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001716	1.00[JPT][hapmap]
rs13006974	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13009586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13018345	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13030953	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1471675	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16846362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17548023	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17552442	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17734546	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17735355	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17735650	0.81[EUR][1000 genomes]
rs17735674	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17791242	1.00[CEU][hapmap]
rs17791266	1.00[CEU][hapmap]
rs17791774	0.81[EUR][1000 genomes]
rs17792070	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1842932	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2890614	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs34050146	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34470585	0.83[EUR][1000 genomes]
rs34531296	1.00[ASN][1000 genomes]
rs34571231	0.96[EUR][1000 genomes]
rs35007711	0.84[EUR][1000 genomes]
rs35148968	0.81[EUR][1000 genomes]
rs35155989	0.81[EUR][1000 genomes]
rs35266942	1.00[ASN][1000 genomes]
rs35390851	1.00[ASN][1000 genomes]
rs36057199	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328578	1.00[ASN][1000 genomes]
rs4340448	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4363970	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4588128	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4635467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs60727330	0.83[EUR][1000 genomes]
rs6429882	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs66461219	0.81[EUR][1000 genomes]
rs66741925	0.93[EUR][1000 genomes]
rs6717454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740704	0.81[EUR][1000 genomes]
rs6741998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6744016	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6746208	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6748629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs73963094	0.83[EUR][1000 genomes]
rs7568338	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7579093	0.84[EUR][1000 genomes]
rs7579392	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7585876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592963	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7592987	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7606229	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv583210	chr2:142259592-142295042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv459629	chr2:142263400-142295042	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv583211	chr2:142263400-142295042	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv583212	chr2:142263979-142309330	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142264000-142266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:142264000-142268000	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:142264200-142266600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:142265800-142266600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr2:142265800-142266600	Enhancers	Brain Substantia Nigra	brain
6	chr2:142265800-142266800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:142266000-142267200	Enhancers	A549	lung
8	chr2:142266200-142267600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:142266200-142267600	Enhancers	Brain Anterior Caudate	brain
10	chr2:142266400-142267200	Enhancers	Brain Cingulate Gyrus	brain

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