Variant report

Variant	rs17240055
Chromosome Location	chr15:57958484-57958485
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	chr15:57957979..57959871-chr15:58003465..58005638,2	K562	blood:
2	chr15:57957919..57960382-chr15:58000140..58002579,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10162772	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11071339	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs11629719	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1346124	0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs1425948	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1425949	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1834488	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2251762	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2433196	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2433197	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2433198	0.90[JPT][hapmap]
rs2554026	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2733601	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs2733602	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[EUR][1000 genomes]
rs2733603	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2733604	0.96[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34270510	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36082771	0.89[EUR][1000 genomes]
rs4578589	0.98[EUR][1000 genomes]
rs4774979	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493939	0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs7169211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176042	0.85[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181013	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs8034146	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]
rs9302201	1.00[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9806740	0.92[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs986868	0.88[CEU][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.93[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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv530682	chr15:57912502-58108285	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17240055	VCL	trans	lymphoblastoid	seeQTL
rs17240055	Gcom1	cis	multi-tissue	Pritchard
rs17240055	MYO1E	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57919400-57959400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:57932200-57967400	Weak transcription	Aorta	Aorta
3	chr15:57933400-57982600	Weak transcription	Esophagus	oesophagus
4	chr15:57947400-57959200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:57949200-57967400	Weak transcription	Right Ventricle	heart
6	chr15:57954000-57959200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:57954800-57958800	Weak transcription	Fetal Kidney	kidney
8	chr15:57955000-57959600	Genic enhancers	Left Ventricle	heart
9	chr15:57955400-57958600	Weak transcription	Stomach Mucosa	stomach
10	chr15:57955400-57964600	Weak transcription	Right Atrium	heart
11	chr15:57955600-57958600	Weak transcription	Fetal Intestine Large	intestine
12	chr15:57955600-57958800	Weak transcription	Fetal Heart	heart
13	chr15:57955600-57959600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:57955600-57960000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:57955600-57967400	Weak transcription	Fetal Lung	lung
16	chr15:57955800-57959400	Weak transcription	Small Intestine	intestine
17	chr15:57955800-57965600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:57955800-57967400	Weak transcription	Gastric	stomach
19	chr15:57956000-57958800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:57956000-57959200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:57956200-57958800	Weak transcription	Fetal Intestine Small	intestine
22	chr15:57957400-57958800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:57957400-57960600	Enhancers	Liver	Liver
24	chr15:57957800-57959200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:57957800-57960400	Enhancers	HMEC	breast
26	chr15:57958000-57958800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:57958000-57959400	Weak transcription	Adipose Nuclei	Adipose
28	chr15:57958000-57959400	Weak transcription	Pancreas	Pancrea
29	chr15:57958200-57960400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:57958400-57959200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr15:57958400-57959200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:57958400-57960200	Enhancers	HSMM	muscle
33	chr15:57958400-57960400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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