Variant report

Variant	rs9288980
Chromosome Location	chr3:112964992-112964993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10511324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13322086	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16860734	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs28679287	0.95[EUR][1000 genomes]
rs3995908	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs6438134	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6763234	1.00[CEU][hapmap]
rs6780720	1.00[CEU][hapmap]
rs6808103	1.00[CEU][hapmap]
rs7625829	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7629636	1.00[CEU][hapmap]
rs7652801	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[EUR][1000 genomes]
rs9810059	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs9819129	0.90[EUR][1000 genomes]
rs9820627	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9823770	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9825012	0.81[EUR][1000 genomes]
rs9831049	0.90[EUR][1000 genomes]
rs9831364	0.90[EUR][1000 genomes]
rs9831793	0.90[EUR][1000 genomes]
rs9837357	0.90[EUR][1000 genomes]
rs9840485	0.90[EUR][1000 genomes]
rs9849714	0.90[TSI][hapmap]
rs9851183	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs9852068	1.00[CEU][hapmap]
rs9853439	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9864630	0.90[EUR][1000 genomes]
rs9869371	0.95[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9288980	SIK1	trans	brain	seeQTL
rs9288980	PHLDB2	trans	brain	seeQTL
rs9288980	PRG4	trans	brain	seeQTL
rs9288980	FAT4	trans	brain	seeQTL
rs9288980	KLF4	trans	brain	seeQTL
rs9288980	OMD	trans	brain	seeQTL
rs9288980	DUSP1	trans	brain	seeQTL
rs9288980	CCL3	trans	brain	seeQTL
rs9288980	CCL3L1	trans	brain	seeQTL
rs9288980	BTG2	trans	brain	seeQTL
rs9288980	TNFRSF11B	trans	brain	seeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
2	chr3:112951200-112967000	Weak transcription	Colonic Mucosa	Colon
3	chr3:112953800-112965600	Weak transcription	Right Atrium	heart
4	chr3:112954200-112965600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:112958600-112969000	Weak transcription	Spleen	Spleen
6	chr3:112960400-112965800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:112960800-112965600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:112960800-112965600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:112960800-112967000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:112961000-112965600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:112961400-112965600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:112961400-112969400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:112961600-112965600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:112961600-112966400	Weak transcription	Fetal Thymus	thymus
15	chr3:112961600-112967400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:112961800-112965400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:112961800-112965600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:112962000-112965600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:112962000-112968200	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:112962000-112968800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:112962200-112965600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:112962400-112969000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:112962800-112968000	Weak transcription	Gastric	stomach
25	chr3:112962800-112972400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:112963000-112965600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:112963000-112965600	Weak transcription	Esophagus	oesophagus
28	chr3:112963000-112968000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:112963000-112969200	Weak transcription	Pancreas	Pancrea
30	chr3:112963000-112972800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:112963600-112965800	Enhancers	Stomach Smooth Muscle	stomach
32	chr3:112963600-112967200	Enhancers	Fetal Lung	lung
33	chr3:112964000-112968000	Enhancers	Fetal Kidney	kidney
34	chr3:112964000-112969000	Enhancers	HSMM	muscle
35	chr3:112964200-112965000	Enhancers	Brain Hippocampus Middle	brain
36	chr3:112964200-112965600	Enhancers	Colon Smooth Muscle	Colon
37	chr3:112964200-112968000	Enhancers	Fetal Stomach	stomach
38	chr3:112964200-112968200	Enhancers	Fetal Muscle Leg	muscle
39	chr3:112964200-112968400	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:112964200-112968800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:112964200-112968800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:112964200-112968800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:112964200-112969400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr3:112964400-112965000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:112964400-112965000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:112964400-112965000	Flanking Active TSS	Osteobl	bone
47	chr3:112964400-112965600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:112964400-112965600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr3:112964400-112967000	Enhancers	NHEK	skin
50	chr3:112964400-112967200	Enhancers	HUES64 Cell Line	embryonic stem cell

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