Variant report

Variant	rs9311432
Chromosome Location	chr3:48850443-48850444
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10780033	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130176	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134591	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11705737	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11705888	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11708022	0.90[ASN][1000 genomes]
rs11709246	0.90[ASN][1000 genomes]
rs11712982	0.87[ASN][1000 genomes]
rs11713694	0.92[ASN][1000 genomes]
rs11717978	0.90[ASN][1000 genomes]
rs11719457	0.90[ASN][1000 genomes]
rs11920534	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924597	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11928552	0.90[CEU][hapmap]
rs12493289	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12493578	0.90[CEU][hapmap]
rs12497850	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs12637037	0.84[EUR][1000 genomes]
rs13064883	0.90[EUR][1000 genomes]
rs13064911	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13072911	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13073997	0.95[ASN][1000 genomes]
rs13076394	0.91[EUR][1000 genomes]
rs13078308	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13086240	0.87[ASN][1000 genomes]
rs13087930	0.90[ASN][1000 genomes]
rs13090839	0.87[ASN][1000 genomes]
rs13094900	0.92[ASN][1000 genomes]
rs13315711	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13316620	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1352420	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs28642807	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34477108	0.90[ASN][1000 genomes]
rs34504524	0.82[ASN][1000 genomes]
rs34509487	0.90[ASN][1000 genomes]
rs3774628	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4072859	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858798	0.90[CEU][hapmap]
rs4858828	0.90[CEU][hapmap]
rs4858831	0.90[CEU][hapmap]
rs4974079	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974080	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4974082	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974084	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4974085	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974087	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974091	0.84[EUR][1000 genomes]
rs55674449	0.83[ASN][1000 genomes]
rs56318350	0.90[ASN][1000 genomes]
rs6414613	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6442130	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6446196	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446198	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6446205	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6446252	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446253	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66653195	0.80[EUR][1000 genomes]
rs67060340	0.95[ASN][1000 genomes]
rs67332931	0.90[ASN][1000 genomes]
rs6768433	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6781790	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6786665	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6788650	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs6789285	0.85[EUR][1000 genomes]
rs6791234	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6791542	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6795025	0.84[EUR][1000 genomes]
rs71324924	0.90[ASN][1000 genomes]
rs7372149	0.83[EUR][1000 genomes]
rs7373778	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7373790	0.83[EUR][1000 genomes]
rs7430198	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430501	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7431710	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7431857	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7612459	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7615235	0.81[EUR][1000 genomes]
rs7615675	0.87[EUR][1000 genomes]
rs7616815	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7621015	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7623023	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626445	0.81[EUR][1000 genomes]
rs7627404	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628719	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7630742	0.86[EUR][1000 genomes]
rs7636057	0.90[EUR][1000 genomes]
rs7639332	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7643368	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7647093	0.86[EUR][1000 genomes]
rs7647813	1.00[CEU][hapmap]
rs7649458	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653459	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8926	0.84[EUR][1000 genomes]
rs9311430	0.95[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311433	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9311434	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9637481	1.00[CEU][hapmap]
rs9681717	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9682444	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9754878	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9755490	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830636	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835307	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840684	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846123	0.84[EUR][1000 genomes]
rs9850134	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867373	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9876848	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879971	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9884022	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs9311432	NCKIPSD	cis	Muscle Skeletal	GTEx
rs9311432	CCDC36	cis	Artery Tibial	GTEx
rs9311432	NICN1-AS1	cis	Thyroid	GTEx
rs9311432	AMT	cis	Muscle Skeletal	GTEx
rs9311432	AMT	cis	Thyroid	GTEx
rs9311432	ARIH2	cis	multi-tissue	Pritchard
rs9311432	WDR6	cis	lung	GTEx
rs9311432	ARIH2	cis	Thyroid	GTEx
rs9311432	NCKIPSD	cis	Whole Blood	GTEx
rs9311432	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9311432	WDR6	cis	Adipose Subcutaneous	GTEx
rs9311432	WDR6	cis	Whole Blood	GTEx
rs9311432	WDR6	cis	Esophagus Mucosa	GTEx
rs9311432	WDR6	cis	Artery Tibial	GTEx
rs9311432	WDR6	cis	Nerve Tibial	GTEx
rs9311432	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs9311432	WDR6	cis	Heart Left Ventricle	GTEx
rs9311432	WDR6	cis	Muscle Skeletal	GTEx
rs9311432	NICN1	cis	Thyroid	GTEx
rs9311432	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs9311432	CCDC36	cis	Esophagus Muscularis	GTEx
rs9311432	NCKIPSD	cis	Nerve Tibial	GTEx
rs9311432	WDR6	cis	Esophagus Muscularis	GTEx
rs9311432	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs9311432	WDR6	cis	uninvolved skin	skin_eQTL
rs9311432	AMT	cis	Whole Blood	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48810000-48882800	Weak transcription	Fetal Brain Female	brain
2	chr3:48820400-48868200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:48820600-48882800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:48821000-48858000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:48821000-48858200	Weak transcription	Gastric	stomach
6	chr3:48822200-48855800	Weak transcription	Lung	lung
7	chr3:48822400-48857800	Weak transcription	NHEK	skin
8	chr3:48822400-48858200	Weak transcription	HSMMtube	muscle
9	chr3:48826400-48868400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:48826800-48858200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:48826800-48869600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:48826800-48882800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:48827000-48850600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:48827800-48858000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:48827800-48865600	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:48831000-48857600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:48831200-48857200	Weak transcription	Ovary	ovary
18	chr3:48831400-48858000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:48833800-48863600	Weak transcription	HSMM	muscle
20	chr3:48834000-48855400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:48842200-48855600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:48842200-48871200	Weak transcription	Fetal Stomach	stomach
23	chr3:48842800-48860600	Weak transcription	Fetal Intestine Small	intestine
24	chr3:48843000-48857200	Weak transcription	Left Ventricle	heart
25	chr3:48843200-48858200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:48847600-48858000	Weak transcription	Hela-S3	cervix
27	chr3:48847600-48858000	Weak transcription	HMEC	breast
28	chr3:48848400-48851000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:48848800-48851000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:48848800-48851400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:48849000-48850800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:48849000-48857200	Weak transcription	Spleen	Spleen
33	chr3:48849000-48858000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:48849200-48850600	Enhancers	Primary T cells from cord blood	blood
35	chr3:48849200-48850800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:48849200-48851000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr3:48849400-48850800	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:48849400-48850800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:48849400-48857800	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:48849600-48857000	Weak transcription	Brain Germinal Matrix	brain
41	chr3:48850000-48850800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:48850000-48850800	Enhancers	Fetal Thymus	thymus
43	chr3:48850200-48850600	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:48850200-48850600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr3:48850200-48850600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr3:48850200-48850600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:48850200-48850600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:48850200-48850600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr3:48850200-48850800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:48850200-48850800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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