Variant report

Variant	rs429969
Chromosome Location	chr4:48356333-48356334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48350227..48353162-chr4:48356080..48357994,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10003230	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026398	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029785	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12507206	0.80[ASN][1000 genomes]
rs12511991	0.80[ASN][1000 genomes]
rs12645501	0.81[JPT][hapmap]
rs12645951	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12649527	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649528	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13105385	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13115295	0.80[ASN][1000 genomes]
rs1352433	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1472967	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1586540	0.81[ASN][1000 genomes]
rs1703973	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1948167	0.81[ASN][1000 genomes]
rs2029348	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291474	1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs2291475	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353312	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35758434	0.81[ASN][1000 genomes]
rs372825	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs382335	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828496	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs392187	0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs403495	0.88[ASN][1000 genomes]
rs404348	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404445	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404656	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411261	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421336	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs421833	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs432927	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445892	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs449376	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450498	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4694895	0.81[ASN][1000 genomes]
rs62309425	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447634	0.81[ASN][1000 genomes]
rs6447635	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816010	0.89[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816352	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829705	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844211	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848073	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848395	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7438704	0.89[ASW][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7668529	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672892	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7674269	0.80[ASN][1000 genomes]
rs7678164	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7683398	0.81[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923372	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923373	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9291323	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs952289	0.81[JPT][hapmap]
rs974014	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974015	0.81[ASN][1000 genomes]
rs974016	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs429969	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL
rs429969	OCIAD2	cis	cerebellum	SCAN
rs429969	SLAIN2	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48362400	Weak transcription	Gastric	stomach
2	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
5	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
6	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
8	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
10	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
11	chr4:48347400-48362200	Weak transcription	NHLF	lung
12	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
14	chr4:48348800-48358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
16	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:48349000-48356600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:48349000-48358400	Weak transcription	HSMM	muscle
19	chr4:48349400-48357200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:48349400-48358000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:48349400-48361800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:48349400-48361800	Weak transcription	HMEC	breast
23	chr4:48349400-48362200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:48349600-48357000	Weak transcription	Lung	lung
25	chr4:48349600-48363200	Weak transcription	Adipose Nuclei	Adipose
26	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
27	chr4:48350000-48358600	Weak transcription	Ovary	ovary
28	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr4:48351400-48361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:48351400-48362600	Weak transcription	A549	lung
31	chr4:48352400-48358400	Weak transcription	NHEK	skin
32	chr4:48352400-48362200	Weak transcription	Left Ventricle	heart
33	chr4:48352800-48358200	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:48353200-48362800	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:48353200-48362800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr4:48353600-48356600	Weak transcription	Psoas Muscle	Psoas
39	chr4:48353600-48358200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:48353600-48358400	Weak transcription	Brain Angular Gyrus	brain
41	chr4:48353600-48362200	Weak transcription	Brain Anterior Caudate	brain
42	chr4:48353600-48362200	Weak transcription	Fetal Heart	heart
43	chr4:48353600-48363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:48353800-48362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
46	chr4:48354400-48356800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:48354800-48356400	Weak transcription	Dnd41	blood
48	chr4:48354800-48362200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:48354800-48362400	Weak transcription	Right Ventricle	heart
50	chr4:48355000-48357800	Weak transcription	K562	blood

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