Variant report

Variant	rs9829181
Chromosome Location	chr3:121663962-121663963
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10934568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11916150	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12489511	0.87[GIH][hapmap]
rs12490565	0.82[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs12695420	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068522	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474327	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1589700	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1919552	0.82[GIH][hapmap]
rs2001391	0.82[GIH][hapmap]
rs2091665	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2141614	0.81[JPT][hapmap]
rs2332056	0.90[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs2689276	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2700424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817599	0.89[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419417	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438689	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770115	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6770719	0.87[GIH][hapmap];0.81[JPT][hapmap]
rs6780559	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626740	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628167	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638094	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646346	0.82[CHB][hapmap]
rs7647751	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289184	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289185	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs953730	0.81[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9815649	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9828757	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9843053	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9829181	SLC15A2	cis	parietal	SCAN
rs9829181	CCDC14	cis	cerebellum	SCAN
rs9829181	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9829181	HCLS1	cis	multi-tissue	Pritchard
rs9829181	SLC15A2	cis	cerebellum	SCAN
rs9829181	MUC13	cis	cerebellum	SCAN
rs9829181	ADPRH	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121615800-121671600	Weak transcription	Pancreas	Pancrea
2	chr3:121627400-121664600	Weak transcription	Aorta	Aorta
3	chr3:121631800-121664800	Weak transcription	Brain Angular Gyrus	brain
4	chr3:121634800-121667000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:121635000-121670600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:121635200-121666800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:121638400-121664800	Weak transcription	Spleen	Spleen
8	chr3:121646800-121666200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:121650600-121665800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:121650600-121675600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:121651200-121664000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:121656400-121667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:121656800-121675200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:121657000-121664600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:121657600-121666000	Strong transcription	Primary B cells from cord blood	blood
16	chr3:121657800-121665200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:121658000-121667000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr3:121660200-121664000	Weak transcription	Primary T cells from cord blood	blood
19	chr3:121660200-121666200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:121660200-121666400	Weak transcription	Lung	lung
21	chr3:121660200-121666800	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:121660200-121670000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:121660200-121671600	Weak transcription	Left Ventricle	heart
24	chr3:121660200-121675200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:121660200-121676600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:121660600-121670400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:121661600-121670000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:121661800-121670200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:121661800-121674800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:121662600-121664000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:121662600-121669800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:121663200-121669400	Weak transcription	GM12878-XiMat	blood
33	chr3:121663200-121669800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:121663600-121664400	Weak transcription	Monocytes-CD14+_RO01746	blood

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