Variant report

Variant	rs17850484
Chromosome Location	chr15:78471110-78471111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78469629..78471471-chr15:78557003..78559345,2	MCF-7	breast:
2	chr15:78439357..78441668-chr15:78468189..78471129,2	MCF-7	breast:
3	chr15:78465805..78468127-chr15:78469824..78472074,2	K562	blood:
4	chr15:78469404..78471342-chr15:78532874..78534838,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166411	Chromatin interaction
ENSG00000140403	Chromatin interaction
ENSG00000103740	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10456	1.00[CHB][hapmap]
rs11854120	1.00[ASN][1000 genomes]
rs11856106	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12440984	1.00[CHB][hapmap]
rs17479031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17850483	1.00[ASN][1000 genomes]
rs2304829	1.00[CHB][hapmap]
rs3825847	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs45444496	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4570804	1.00[ASN][1000 genomes]
rs57867560	1.00[ASN][1000 genomes]
rs62009333	1.00[ASN][1000 genomes]
rs62009334	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62009335	1.00[ASN][1000 genomes]
rs62009337	1.00[ASN][1000 genomes]
rs62009339	1.00[ASN][1000 genomes]
rs62009340	1.00[ASN][1000 genomes]
rs62009342	1.00[ASN][1000 genomes]
rs62009343	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62009344	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62009346	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165154	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8026525	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78460200-78474200	Weak transcription	HepG2	liver
3	chr15:78464800-78475000	Weak transcription	HMEC	breast
4	chr15:78465200-78474200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:78465400-78475200	Weak transcription	NHEK	skin
9	chr15:78466800-78473200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:78466800-78473400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:78467000-78473200	Weak transcription	Aorta	Aorta
12	chr15:78467000-78473200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:78467000-78473400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:78467200-78477200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:78467400-78474800	Weak transcription	Fetal Brain Female	brain
16	chr15:78467400-78475400	Enhancers	Fetal Thymus	thymus
17	chr15:78467600-78472000	Weak transcription	Spleen	Spleen
18	chr15:78468400-78471200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:78469800-78471200	Enhancers	Fetal Muscle Leg	muscle
20	chr15:78469800-78471400	Enhancers	Fetal Muscle Trunk	muscle
21	chr15:78470000-78472400	Genic enhancers	Thymus	Thymus
22	chr15:78470200-78471800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:78470200-78477000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:78470200-78486600	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:78470400-78493800	Weak transcription	Brain Substantia Nigra	brain
26	chr15:78470600-78477200	Weak transcription	Brain Anterior Caudate	brain
27	chr15:78470600-78486600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr15:78470800-78471600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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