Variant report

Variant	rs9311431
Chromosome Location	chr3:48848787-48848788
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10865953	1.00[CEU][hapmap]
rs11707968	0.85[EUR][1000 genomes]
rs12632533	1.00[CEU][hapmap]
rs12715430	0.87[EUR][1000 genomes]
rs14018	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4858800	1.00[CEU][hapmap]
rs4858830	1.00[CEU][hapmap]
rs4974083	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4974088	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6442131	0.88[EUR][1000 genomes]
rs6446200	0.81[EUR][1000 genomes]
rs6446204	1.00[CEU][hapmap]
rs6766238	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6772452	1.00[CEU][hapmap]
rs6796790	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6801211	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6806356	1.00[CEU][hapmap]
rs7373072	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7429596	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7434187	1.00[CEU][hapmap]
rs7611628	0.82[EUR][1000 genomes]
rs7621226	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7639370	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7641050	0.81[EUR][1000 genomes]
rs7653408	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9284885	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9848268	0.81[EUR][1000 genomes]
rs9859473	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9864243	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9873227	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9879978	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9882443	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs990211	0.81[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9311431	NICN1-AS1	cis	Thyroid	GTEx
rs9311431	AMT	cis	Adipose Subcutaneous	GTEx
rs9311431	AMT	cis	Artery Aorta	GTEx
rs9311431	WDR6	cis	Muscle Skeletal	GTEx
rs9311431	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9311431	AMT	cis	Esophagus Mucosa	GTEx
rs9311431	NICN1	cis	Thyroid	GTEx
rs9311431	AMT	cis	lung	GTEx
rs9311431	P4HTM	cis	lung	GTEx
rs9311431	AMT	cis	Whole Blood	GTEx
rs9311431	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs9311431	AMT	cis	Thyroid	GTEx
rs9311431	AMT	cis	Artery Tibial	GTEx
rs9311431	AMT	cis	Nerve Tibial	GTEx
rs9311431	WDR6	cis	Nerve Tibial	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48809000-48849400	Weak transcription	GM12878-XiMat	blood
2	chr3:48810000-48882800	Weak transcription	Fetal Brain Female	brain
3	chr3:48820400-48868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:48820600-48882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:48821000-48849000	Weak transcription	NHLF	lung
6	chr3:48821000-48858000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:48821000-48858200	Weak transcription	Gastric	stomach
8	chr3:48822200-48855800	Weak transcription	Lung	lung
9	chr3:48822400-48857800	Weak transcription	NHEK	skin
10	chr3:48822400-48858200	Weak transcription	HSMMtube	muscle
11	chr3:48826400-48868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:48826800-48848800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:48826800-48858200	Weak transcription	Brain Angular Gyrus	brain
14	chr3:48826800-48869600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:48826800-48882800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:48827000-48848800	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:48827000-48850600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:48827600-48850200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:48827800-48858000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:48827800-48865600	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:48828000-48849400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:48828200-48848800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:48828400-48849600	Weak transcription	Osteobl	bone
24	chr3:48831000-48857600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:48831200-48857200	Weak transcription	Ovary	ovary
26	chr3:48831400-48849200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:48831400-48858000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:48833800-48863600	Weak transcription	HSMM	muscle
29	chr3:48834000-48855400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:48834200-48849000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:48835200-48849400	Weak transcription	Primary B cells from cord blood	blood
32	chr3:48842200-48855600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:48842200-48871200	Weak transcription	Fetal Stomach	stomach
34	chr3:48842800-48860600	Weak transcription	Fetal Intestine Small	intestine
35	chr3:48843000-48857200	Weak transcription	Left Ventricle	heart
36	chr3:48843200-48850200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:48843200-48858200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:48843600-48849200	Weak transcription	Brain Substantia Nigra	brain
39	chr3:48847200-48849600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr3:48847400-48849000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:48847600-48848800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:48847600-48848800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:48847600-48849000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:48847600-48849200	Weak transcription	Primary T cells from cord blood	blood
45	chr3:48847600-48849200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:48847600-48849200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:48847600-48849400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:48847600-48849600	Enhancers	Brain Germinal Matrix	brain
49	chr3:48847600-48850000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:48847600-48858000	Weak transcription	Hela-S3	cervix

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