Variant report

Variant	rs4419357
Chromosome Location	chr3:43286041-43286042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11129996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11927798	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12715387	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12715388	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059783	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060695	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13066699	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13074235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13085652	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316297	0.96[ASN][1000 genomes]
rs1320156	0.94[ASN][1000 genomes]
rs1320158	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1573931	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17075317	0.86[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs17075335	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17075378	0.94[ASN][1000 genomes]
rs17075381	0.94[ASN][1000 genomes]
rs17075398	0.96[ASN][1000 genomes]
rs1814902	0.88[ASN][1000 genomes]
rs2372352	0.90[ASN][1000 genomes]
rs2372354	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2372355	0.94[ASN][1000 genomes]
rs2372356	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2888295	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2888296	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4016130	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4260403	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4404425	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4444688	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4637262	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682675	0.91[ASN][1000 genomes]
rs4682872	0.93[ASN][1000 genomes]
rs4682879	0.91[ASN][1000 genomes]
rs4683363	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683364	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap]
rs4683367	0.90[ASN][1000 genomes]
rs4683369	0.93[ASN][1000 genomes]
rs6442144	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6762503	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6781696	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6798619	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6805075	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621298	0.85[JPT][hapmap]
rs7621511	0.94[ASN][1000 genomes]
rs7627198	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636673	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7639584	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7639605	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648154	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9311334	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9311335	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311336	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9681394	0.85[JPT][hapmap]
rs9683242	0.82[JPT][hapmap]
rs9809273	0.94[ASN][1000 genomes]
rs9820946	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9822961	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9826102	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9826849	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9827911	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833793	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9852399	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9853795	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9858012	0.91[CHB][hapmap];0.84[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9860007	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9860364	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861337	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861529	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9875582	0.95[CHD][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834672	chr3:43132722-43306272	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4419357	SLC25A38	cis	parietal	SCAN
rs4419357	SNRK	cis	cerebellum	SCAN
rs4419357	FYCO1	cis	parietal	SCAN
rs4419357	PTH1R	cis	parietal	SCAN
rs4419357	RPL14	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43284200-43286400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:43284200-43289800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr3:43284400-43288400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:43284400-43289800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:43284400-43290000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr3:43284400-43290000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:43284400-43290400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:43284400-43300400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:43284600-43287400	Enhancers	Fetal Muscle Leg	muscle
10	chr3:43284600-43289400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:43284600-43290000	Enhancers	Primary T cells from cord blood	blood
12	chr3:43284800-43289400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:43285000-43286200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:43285000-43288000	Enhancers	HUVEC	blood vessel
15	chr3:43285000-43289600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:43285000-43289600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:43285200-43286400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:43285200-43286400	Enhancers	Spleen	Spleen
19	chr3:43285200-43286600	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:43285200-43286800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:43285200-43286800	Enhancers	Psoas Muscle	Psoas
22	chr3:43285200-43290000	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:43285400-43286200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:43285400-43290000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:43285600-43286400	Enhancers	Duodenum Mucosa	Duodenum
26	chr3:43285600-43287200	Weak transcription	Primary B cells from cord blood	blood
27	chr3:43285600-43290800	Enhancers	Adipose Nuclei	Adipose
28	chr3:43285800-43286200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:43285800-43288400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:43285800-43289200	Weak transcription	Lung	lung
31	chr3:43285800-43298400	Weak transcription	Left Ventricle	heart
32	chr3:43286000-43287200	Weak transcription	Thymus	Thymus
33	chr3:43286000-43288000	Weak transcription	Fetal Thymus	thymus
34	chr3:43286000-43289600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:43286000-43289800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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