Variant report

Variant	rs2664140
Chromosome Location	chr15:39832122-39832123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1038097	0.97[EUR][1000 genomes]
rs1051442	0.92[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs10520139	1.00[CHD][hapmap]
rs10520141	0.92[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs10520143	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10520146	0.84[CEU][hapmap]
rs1382443	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs1382444	0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs1551946	1.00[CHD][hapmap]
rs16969487	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs16969491	0.90[EUR][1000 genomes]
rs16969546	1.00[CHD][hapmap]
rs16969559	1.00[CHD][hapmap]
rs16969560	1.00[CHD][hapmap]
rs17632916	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633107	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs17633210	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs17705806	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17706083	0.92[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs17706179	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1813493	0.97[EUR][1000 genomes]
rs1988082	0.90[EUR][1000 genomes]
rs1988555	0.91[EUR][1000 genomes]
rs2228263	0.92[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2411316	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2618156	0.97[EUR][1000 genomes]
rs2618157	0.93[AFR][1000 genomes]
rs2618160	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618161	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs2618164	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2618165	0.92[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2618167	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs2664123	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2664136	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664137	0.97[EUR][1000 genomes]
rs2664138	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664142	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377784	0.91[EUR][1000 genomes]
rs28549326	0.91[EUR][1000 genomes]
rs28619289	0.91[EUR][1000 genomes]
rs28653011	0.91[EUR][1000 genomes]
rs34878675	0.85[EUR][1000 genomes]
rs41315060	0.93[EUR][1000 genomes]
rs4415979	0.92[CEU][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs4503768	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs45461294	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923835	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs58188999	0.91[EUR][1000 genomes]
rs59578395	0.94[EUR][1000 genomes]
rs59628570	0.84[EUR][1000 genomes]
rs6492905	0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs74008647	0.91[EUR][1000 genomes]
rs74008648	0.91[EUR][1000 genomes]
rs8024038	1.00[CHD][hapmap]
rs880270	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs954152	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985808	0.81[EUR][1000 genomes]
rs9972350	0.92[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2664140	CHD4	trans	parietal	SCAN
rs2664140	CASC5	cis	parietal	SCAN
rs2664140	WNT11	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39823600-39835400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:39826000-39833200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:39831000-39832600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:39831000-39832600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:39831200-39832800	Enhancers	Ovary	ovary
6	chr15:39831600-39832800	Enhancers	Colon Smooth Muscle	Colon
7	chr15:39831800-39832600	Enhancers	Rectal Smooth Muscle	rectum
8	chr15:39832000-39833000	Enhancers	Thymus	Thymus

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