Variant report

Variant	rs1963072
Chromosome Location	chr5:100003859-100003860
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:99993129..99995264-chr5:100001992..100004177,2	K562	blood:

Variant related genes	Relation type
ENSG00000250806	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11741121	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514770	0.93[ASN][1000 genomes]
rs13160690	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1445173	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1962921	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963465	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2055617	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2590413	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2590420	0.89[EUR][1000 genomes]
rs2590421	0.89[EUR][1000 genomes]
rs2590422	0.91[EUR][1000 genomes]
rs2590423	0.91[EUR][1000 genomes]
rs2590424	0.91[EUR][1000 genomes]
rs2725107	0.91[EUR][1000 genomes]
rs2725110	0.91[EUR][1000 genomes]
rs6595366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595380	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6865946	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6866306	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6879808	0.93[ASN][1000 genomes]
rs6880868	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6886596	0.93[ASN][1000 genomes]
rs6888825	0.94[ASN][1000 genomes]
rs7701876	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7702043	0.84[EUR][1000 genomes]
rs7707450	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7718146	0.93[ASN][1000 genomes]
rs7736625	0.92[ASN][1000 genomes]
rs7738040	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer 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	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv882466	chr5:99936090-100029620	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv882467	chr5:99952282-100100157	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv599174	chr5:99959205-100006633	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv882468	chr5:99959205-100029620	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1019974	chr5:99968378-100010033	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1963072	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99999800-100004600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr5:100000200-100004200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:100001800-100004000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:100001800-100004000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:100002000-100004600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr5:100002200-100004000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:100002400-100004000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr5:100002400-100004000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr5:100002400-100004800	Enhancers	HUVEC	blood vessel
10	chr5:100002600-100004600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:100002600-100005000	Enhancers	HMEC	breast
12	chr5:100002800-100004000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr5:100002800-100004000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr5:100002800-100004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:100002800-100004600	Enhancers	Hela-S3	cervix
16	chr5:100002800-100004600	Enhancers	NHEK	skin
17	chr5:100002800-100004600	Enhancers	Osteobl	bone
18	chr5:100002800-100005000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:100003200-100004000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:100003600-100004000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr5:100003600-100004000	Enhancers	NH-A	brain
22	chr5:100003600-100004200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:100003800-100005200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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