Variant report

Variant	rs3959644
Chromosome Location	chr15:45488132-45488133
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45487345..45489063-chr15:45489190..45491924,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259932	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10775129	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10851421	0.82[ASN][1000 genomes]
rs10851422	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10851423	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11070444	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12323957	0.88[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12437603	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12438755	0.91[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12440238	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12440321	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12440793	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12592055	0.81[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[MKK][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12593605	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12899786	0.86[ASW][hapmap];0.95[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12901114	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12902212	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903149	0.83[AMR][1000 genomes]
rs12904079	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904265	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12904331	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12904815	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12905053	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905246	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12906537	0.85[AMR][1000 genomes]
rs12906734	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12908943	0.80[EUR][1000 genomes]
rs12909987	0.81[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs12910270	0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12910591	0.80[ASN][1000 genomes]
rs12913123	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12915027	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12915804	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12915965	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1648302	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1648311	0.95[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1706804	0.95[CEU][hapmap]
rs1706821	0.96[EUR][1000 genomes]
rs1706822	0.96[EUR][1000 genomes]
rs2292467	0.95[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs2433229	0.82[CEU][hapmap]
rs2458236	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs2467838	0.98[EUR][1000 genomes]
rs2899378	0.84[AMR][1000 genomes]
rs2899379	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3759892	0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4439707	0.85[AMR][1000 genomes]
rs60001836	0.80[EUR][1000 genomes]
rs62026661	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62026665	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62026666	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167731	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7171401	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7174913	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs753414	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs8040896	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3959644	ADAL	cis	parietal	SCAN
rs3959644	SHF	cis	parietal	SCAN
rs3959644	FSIP1	cis	parietal	SCAN
rs3959644	SHF	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45481000-45490200	Weak transcription	Ovary	ovary
2	chr15:45481000-45490600	Weak transcription	Colonic Mucosa	Colon
3	chr15:45481200-45490200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:45481200-45490400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:45482000-45490000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:45486000-45489400	Weak transcription	HepG2	liver
7	chr15:45487600-45488200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr15:45487800-45488200	Enhancers	H9 Cell Line	embryonic stem cell

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