Variant report

Variant	rs3860990
Chromosome Location	chr9:33467595-33467596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:33467112-33467857	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:33410830..33412898-chr9:33466360..33468134,2	MCF-7	breast:
2	chr9:33465669..33469321-chr9:33471181..33475399,6	K562	blood:
3	chr9:33401937..33405021-chr9:33465518..33470262,4	MCF-7	breast:
4	chr9:33444170..33447177-chr9:33466129..33468559,3	MCF-7	breast:

Variant related genes	Relation type
NOL6	TF binding region
ENSG00000223678	Chromatin interaction
ENSG00000165269	Chromatin interaction
ENSG00000165271	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17253468	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs56108788	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57867764	0.84[EUR][1000 genomes]
rs7022355	0.85[EUR][1000 genomes]
rs72709610	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72709611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72709612	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72709613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72709621	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72709624	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72709629	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72709632	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72709635	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024207	chr9:33296368-33574892	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1024571	chr9:33380148-33468682	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1015928	chr9:33386067-33468682	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
4	nsv518168	chr9:33465182-33478434	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv527128	chr9:33465651-33467595	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3860990	NOL6	cis	cerebellum	SCAN
rs3860990	CCL21	cis	parietal	SCAN
rs3860990	RNF38	cis	cerebellum	SCAN
rs3860990	AQP3	cis	cerebellum	SCAN
rs3860990	APTX	cis	parietal	SCAN
rs3860990	PRSS3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:33448400-33473000	Weak transcription	Right Atrium	heart
2	chr9:33453000-33469400	Weak transcription	Fetal Heart	heart
3	chr9:33453600-33473200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:33459400-33472200	Strong transcription	Fetal Brain Female	brain
5	chr9:33459600-33472200	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:33459800-33468200	Weak transcription	Fetal Brain Male	brain
7	chr9:33460000-33470400	Strong transcription	Thymus	Thymus
8	chr9:33460000-33470600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:33460000-33472000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr9:33460000-33472000	Strong transcription	Fetal Stomach	stomach
11	chr9:33460000-33472200	Strong transcription	Fetal Intestine Large	intestine
12	chr9:33460000-33472200	Strong transcription	Fetal Intestine Small	intestine
13	chr9:33460000-33472200	Strong transcription	Fetal Muscle Leg	muscle
14	chr9:33460200-33471400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:33460200-33471600	Strong transcription	HSMM	muscle
16	chr9:33460200-33471800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:33460200-33471800	Strong transcription	Brain Germinal Matrix	brain
18	chr9:33460200-33471800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:33460200-33471800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr9:33460200-33472000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:33460200-33472000	Strong transcription	Brain Anterior Caudate	brain
22	chr9:33460200-33472000	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:33460200-33472000	Strong transcription	Placenta	Placenta
24	chr9:33460200-33472000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr9:33460200-33472200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:33460200-33472200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:33460200-33472400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:33460400-33470800	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr9:33460400-33471200	Strong transcription	Primary T cells from cord blood	blood
30	chr9:33460400-33471200	Strong transcription	NH-A	brain
31	chr9:33460400-33471400	Strong transcription	Brain Angular Gyrus	brain
32	chr9:33460400-33471600	Strong transcription	Osteobl	bone
33	chr9:33460400-33472000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr9:33460400-33472000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr9:33460400-33472000	Strong transcription	Brain Cingulate Gyrus	brain
36	chr9:33460400-33472000	Strong transcription	Gastric	stomach
37	chr9:33460400-33472200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr9:33460400-33472200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:33460400-33472200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:33460600-33470400	Strong transcription	Spleen	Spleen
41	chr9:33460600-33470800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:33460600-33471400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:33460600-33471600	Strong transcription	GM12878-XiMat	blood
44	chr9:33460600-33471800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:33460600-33471800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr9:33460600-33472000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:33460600-33472200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr9:33460600-33472200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:33460600-33472200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:33460600-33472200	Strong transcription	Primary B cells from peripheral blood	blood

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