Variant report

Variant	rs9934579
Chromosome Location	chr16:30474856-30474857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30453913..30457972-chr16:30471987..30476748,6	K562	blood:
2	chr16:30454956..30458166-chr16:30472529..30475515,3	MCF-7	breast:
3	chr16:30455690..30457972-chr16:30473175..30475759,2	K562	blood:
4	chr16:30453410..30455041-chr16:30474249..30476075,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179918	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10871452	0.87[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs11862597	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17790906	1.00[GIH][hapmap]
rs17839544	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2230434	1.00[GIH][hapmap]
rs35069260	0.85[EUR][1000 genomes]
rs55919902	0.99[EUR][1000 genomes]
rs67575585	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7195241	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
4	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
5	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
6	nsv1783	chr16:30449450-30494321	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9934579	CLN3	cis	parietal	SCAN
rs9934579	PRR14	cis	parietal	SCAN
rs9934579	SEZ6L2	cis	Cerebellum	GTEx
rs9934579	BCL7C	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30469400-30477000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr16:30470600-30479200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:30470600-30485000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:30471000-30477200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr16:30471200-30476600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr16:30471200-30476600	Weak transcription	Dnd41	blood
7	chr16:30471200-30476800	Weak transcription	Primary T cells from cord blood	blood
8	chr16:30471200-30476800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:30471200-30477000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr16:30471200-30477200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr16:30471200-30477200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:30472600-30475400	Weak transcription	HepG2	liver
13	chr16:30473200-30476600	Weak transcription	Thymus	Thymus
14	chr16:30473200-30477200	Weak transcription	GM12878-XiMat	blood
15	chr16:30473400-30475400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr16:30473400-30476800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr16:30473400-30479400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:30473600-30475200	Weak transcription	Fetal Thymus	thymus
19	chr16:30473600-30476600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr16:30473600-30477200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr16:30473600-30477400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr16:30473600-30482000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr16:30473600-30482000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr16:30473800-30475000	Weak transcription	Monocytes-CD14+_RO01746	blood

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