Variant report

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16878397	1.00[LWK][hapmap]
rs187481	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs206789	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs286153	0.85[MEX][hapmap]
rs286154	0.85[MEX][hapmap]
rs286156	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs286158	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4307050	0.90[CEU][hapmap]
rs4326096	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4515250	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap]
rs4699956	1.00[LWK][hapmap]
rs4699959	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5012862	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6449478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6449480	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6449484	1.00[CEU][hapmap];0.93[TSI][hapmap]
rs6877561	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6896680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap]
rs6896942	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7725028	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription 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	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2409791	ZSWIM6	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59873000-59908600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:59873000-59908800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:59873200-59911000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:59874600-59889600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:59874600-59890400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:59875400-59895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:59875400-59895800	Weak transcription	Fetal Thymus	thymus
8	chr5:59875400-59899400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:59875400-59911000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:59876400-59890600	Weak transcription	Dnd41	blood
11	chr5:59879000-59886000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:59882200-59884600	Weak transcription	Primary B cells from cord blood	blood
13	chr5:59882200-59890400	Weak transcription	Fetal Intestine Large	intestine
14	chr5:59882200-59890400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:59882200-59890800	Weak transcription	HepG2	liver
16	chr5:59883400-59893600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:59883400-59894200	Weak transcription	Placenta	Placenta

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