Variant report

Variant	rs9859473
Chromosome Location	chr3:48837182-48837183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10865953	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs11707968	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12632533	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs12715430	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858800	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4858830	1.00[CEU][hapmap]
rs4974083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6442131	0.89[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs6766238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6796790	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs7373072	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7429596	0.90[EUR][1000 genomes]
rs7434187	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs7610519	0.81[EUR][1000 genomes]
rs7611628	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7639370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7641050	0.81[EUR][1000 genomes]
rs7653408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9311431	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9848268	0.80[EUR][1000 genomes]
rs9864243	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9873227	0.92[EUR][1000 genomes]
rs9879978	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs990211	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487342	chr3:48823957-48960475	Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	esv3487343	chr3:48823963-48960381	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs9859473	NICN1	cis	multi-tissue	Pritchard
rs9859473	ZNF589	cis	parietal	SCAN
rs9859473	DALRD3	cis	parietal	SCAN
rs9859473	AMT	cis	Artery Tibial	GTEx
rs9859473	WDR6	cis	cerebellum	SCAN
rs9859473	IQCF1	cis	cerebellum	SCAN
rs9859473	NICN1-AS1	cis	Thyroid	GTEx
rs9859473	QRICH1	cis	cerebellum	SCAN
rs9859473	LZTFL1	cis	cerebellum	SCAN
rs9859473	WDR6	cis	Nerve Tibial	GTEx
rs9859473	AMT	cis	Nerve Tibial	GTEx
rs9859473	WDR6	cis	Muscle Skeletal	GTEx
rs9859473	GPX1	cis	parietal	SCAN
rs9859473	AMT	cis	lung	GTEx
rs9859473	NICN1	cis	Thyroid	GTEx
rs9859473	AMT	cis	parietal	SCAN
rs9859473	PHF7	cis	parietal	SCAN
rs9859473	AMT	cis	lymphoblastoid	seeQTL
rs9859473	AMT	cis	cerebellum	SCAN
rs9859473	AMT	cis	Whole Blood	GTEx
rs9859473	WDR6	cis	multi-tissue	Pritchard
rs9859473	DALRD3	cis	cerebellum	SCAN
rs9859473	ARIH2	cis	Thyroid	GTEx
rs9859473	AMT	cis	multi-tissue	Pritchard
rs9859473	NCKIPSD	cis	Nerve Tibial	GTEx
rs9859473	WDR6	cis	parietal	SCAN
rs9859473	P4HTM	cis	parietal	SCAN
rs9859473	AMT	cis	Thyroid	GTEx
rs9859473	NICN1	cis	parietal	SCAN
rs9859473	TLR9	cis	parietal	SCAN
rs9859473	AMT	cis	Adipose Subcutaneous	GTEx
rs9859473	AMT	cis	Artery Aorta	GTEx
rs9859473	NCKIPSD	cis	parietal	SCAN
rs9859473	NCKIPSD	cis	multi-tissue	Pritchard
rs9859473	NICN1	cis	cerebellum	SCAN
rs9859473	P4HTM	cis	lung	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48789400-48844000	Weak transcription	Fetal Lung	lung
2	chr3:48809000-48849400	Weak transcription	GM12878-XiMat	blood
3	chr3:48810000-48882800	Weak transcription	Fetal Brain Female	brain
4	chr3:48810400-48848600	Weak transcription	Brain Anterior Caudate	brain
5	chr3:48810600-48842600	Weak transcription	Pancreas	Pancrea
6	chr3:48820400-48868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:48820600-48840200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:48820600-48882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:48820800-48843200	Weak transcription	Right Ventricle	heart
10	chr3:48820800-48847200	Weak transcription	NHDF-Ad	bronchial
11	chr3:48821000-48840600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:48821000-48849000	Weak transcription	NHLF	lung
13	chr3:48821000-48858000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:48821000-48858200	Weak transcription	Gastric	stomach
15	chr3:48822200-48843600	Weak transcription	Fetal Intestine Large	intestine
16	chr3:48822200-48855800	Weak transcription	Lung	lung
17	chr3:48822400-48848600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:48822400-48857800	Weak transcription	NHEK	skin
19	chr3:48822400-48858200	Weak transcription	HSMMtube	muscle
20	chr3:48824000-48842800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:48825800-48837800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:48826400-48868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:48826600-48842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:48826800-48841000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:48826800-48842000	Weak transcription	Aorta	Aorta
26	chr3:48826800-48842400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:48826800-48847200	Weak transcription	Primary T cells from cord blood	blood
28	chr3:48826800-48847200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:48826800-48847200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:48826800-48847200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:48826800-48847600	Weak transcription	Brain Germinal Matrix	brain
32	chr3:48826800-48848800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:48826800-48858200	Weak transcription	Brain Angular Gyrus	brain
34	chr3:48826800-48869600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:48826800-48882800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:48827000-48847200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:48827000-48847200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:48827000-48848800	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:48827000-48850600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr3:48827600-48845200	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:48827600-48850200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:48827800-48842600	Weak transcription	Left Ventricle	heart
43	chr3:48827800-48847400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:48827800-48848200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr3:48827800-48858000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:48827800-48865600	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:48828000-48841400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:48828000-48846600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:48828000-48849400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:48828200-48842000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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