Variant report

Variant	rs2438627
Chromosome Location	chr5:79398016-79398017
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79397094..79398973-chr5:79550751..79553647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164300	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13158441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs13158559	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1465852	0.90[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2099651	0.96[CEU][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2434289	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2434290	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2434291	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2434293	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434294	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2434295	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2438624	0.89[EUR][1000 genomes]
rs2438626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv598744	chr5:79388745-79423347	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2438627	SPZ1	cis	cerebellum	SCAN
rs2438627	JMY	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79379400-79400600	Weak transcription	Left Ventricle	heart
2	chr5:79388000-79405000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:79389400-79412200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:79389600-79398400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr5:79389800-79411800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:79390000-79401200	Weak transcription	Pancreas	Pancrea
7	chr5:79390600-79405400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:79390800-79402000	Weak transcription	Right Atrium	heart
9	chr5:79393400-79410800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:79393600-79399000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:79393800-79405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:79395200-79398400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:79395200-79399200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:79395200-79401800	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:79395800-79398200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:79395800-79400400	Weak transcription	HepG2	liver
17	chr5:79396000-79406200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:79397400-79404000	Enhancers	Fetal Thymus	thymus
19	chr5:79397600-79398600	Enhancers	GM12878-XiMat	blood
20	chr5:79397600-79402000	Enhancers	Primary T cells from cord blood	blood
21	chr5:79397600-79402400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:79397800-79403000	Enhancers	Thymus	Thymus
23	chr5:79398000-79402800	Enhancers	Fetal Heart	heart

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