Variant report

Variant	rs17702560
Chromosome Location	chr3:116028664-116028665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:116023706..116025318-chr3:116027363..116029556,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13066016	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13069169	0.84[EUR][1000 genomes]
rs13083485	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13084538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089698	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13090417	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13100898	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1346944	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16824766	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17645807	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702806	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34126529	0.88[EUR][1000 genomes]
rs34279063	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34408946	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34905742	0.94[EUR][1000 genomes]
rs35538266	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35966018	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71323438	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71323439	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs960082	0.97[EUR][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	nsv3957	chr3:115986950-116032625	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv877361	chr3:116017931-116138039	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116017000-116029600	Enhancers	Colon Smooth Muscle	Colon
2	chr3:116019600-116037000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:116022200-116033000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:116026000-116031600	Weak transcription	Brain Angular Gyrus	brain
5	chr3:116026000-116031600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:116026200-116037200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:116026400-116034000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:116027000-116028800	Enhancers	Brain Substantia Nigra	brain
9	chr3:116027400-116028800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:116028200-116037400	Weak transcription	Brain Germinal Matrix	brain
11	chr3:116028400-116029200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:116028400-116029400	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:116028600-116029200	Enhancers	Brain Anterior Caudate	brain
14	chr3:116028600-116029400	Enhancers	Rectal Smooth Muscle	rectum

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