Variant report

Variant	rs279743
Chromosome Location	chr5:53415114-53415115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53413797..53417195-chr5:53423854..53425574,3	MCF-7	breast:
2	chr5:53414031..53418111-chr5:53418670..53421510,3	K562	blood:
3	chr5:53411323..53415710-chr5:53607730..53609882,4	K562	blood:
4	chr5:53414419..53416796-chr5:53420283..53421795,2	MCF-7	breast:
5	chr5:53414031..53416832-chr5:53418670..53420660,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12054756	0.92[YRI][hapmap]
rs1345815	0.83[CHD][hapmap]
rs154020	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs154041	0.80[ASN][1000 genomes]
rs156825	0.93[CHB][hapmap];0.80[JPT][hapmap]
rs156830	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs157069	0.80[ASN][1000 genomes]
rs157072	0.82[ASN][1000 genomes]
rs16882227	0.84[YRI][hapmap]
rs16882414	0.86[CHD][hapmap]
rs16882451	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs202168	0.93[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs244643	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2457162	0.80[AMR][1000 genomes]
rs2547538	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs26608	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs26609	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs26610	0.93[CHB][hapmap];0.95[ASN][1000 genomes]
rs26775	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs277320	0.80[ASN][1000 genomes]
rs277321	0.80[ASN][1000 genomes]
rs277323	0.87[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs277325	0.80[ASN][1000 genomes]
rs277327	0.80[ASN][1000 genomes]
rs277328	0.80[ASN][1000 genomes]
rs277329	0.87[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs277330	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs27776	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs278065	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs278066	0.80[ASN][1000 genomes]
rs27897	0.93[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs279744	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs28033	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs35006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs35545340	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3797254	0.86[CHB][hapmap]
rs3797255	0.87[CHD][hapmap]
rs3843452	0.86[CHB][hapmap]
rs464888	0.87[CHB][hapmap]
rs4865808	0.86[CHB][hapmap]
rs4865809	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs682103	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6866862	0.86[CHB][hapmap]
rs700915	0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1015340	chr5:53326385-53471882	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats 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	12 gene(s)	inside rSNPs	diseases
19	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
20	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
21	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs279743	ISL1	cis	parietal	SCAN
rs279743	GPX8	cis	cerebellum	SCAN
rs279743	HSPB3	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53389400-53416400	Weak transcription	Left Ventricle	heart
2	chr5:53408200-53416200	Weak transcription	HSMM	muscle
3	chr5:53409000-53416400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:53409200-53448000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:53409200-53465600	Weak transcription	Fetal Intestine Large	intestine
6	chr5:53409400-53423800	Weak transcription	Primary T cells from cord blood	blood
7	chr5:53409600-53441200	Weak transcription	Primary B cells from cord blood	blood
8	chr5:53412200-53415400	Weak transcription	HSMMtube	muscle
9	chr5:53412400-53416200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:53412600-53416400	Weak transcription	NHDF-Ad	bronchial
11	chr5:53413000-53417000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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