Variant report

Variant	rs411261
Chromosome Location	chr4:48354057-48354058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48351553..48354497-chr4:48357846..48360207,2	MCF-7	breast:
2	chr4:48337400..48346343-chr4:48347805..48355704,14	K562	blood:
3	chr4:48342571..48344149-chr4:48352439..48354325,2	MCF-7	breast:
4	chr4:48349775..48352299-chr4:48353081..48355903,3	K562	blood:
5	chr4:48353391..48356261-chr4:48359560..48361635,3	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10003230	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026398	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10029785	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[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];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12507206	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12511991	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12645501	0.81[JPT][hapmap]
rs12645951	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[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];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12649527	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12649528	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13105385	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13115295	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13133788	0.81[EUR][1000 genomes]
rs13148849	0.82[EUR][1000 genomes]
rs13150017	0.81[EUR][1000 genomes]
rs1352433	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1472967	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1586540	0.81[ASN][1000 genomes]
rs1703973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1948167	0.81[ASN][1000 genomes]
rs2029348	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291474	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2291475	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2353312	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28409655	0.83[EUR][1000 genomes]
rs35758434	0.81[ASN][1000 genomes]
rs372825	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs382335	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828496	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs392187	0.87[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs403495	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs404348	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404445	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404656	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421336	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs421833	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs429969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432927	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445892	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs449376	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs450498	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4694895	0.81[ASN][1000 genomes]
rs62309425	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447634	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6447635	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816010	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[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];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816352	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829705	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844211	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848073	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848395	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7438704	0.89[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7668529	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7672892	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7674269	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7678164	0.92[AMR][1000 genomes];0.92[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];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs923372	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923373	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9291323	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs952289	0.81[JPT][hapmap]
rs974014	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974015	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs974016	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.95[AMR][1000 genomes];0.93[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
rs411261	OCIAD2	cis	cerebellum	SCAN
rs411261	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL
rs411261	SLAIN2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48354400	Weak transcription	Esophagus	oesophagus
2	chr4:48344800-48362400	Weak transcription	Gastric	stomach
3	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:48346200-48354600	Weak transcription	Fetal Intestine Small	intestine
7	chr4:48346200-48356200	Weak transcription	Fetal Thymus	thymus
8	chr4:48346200-48356600	Weak transcription	HUVEC	blood vessel
9	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
10	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
12	chr4:48346600-48354800	Weak transcription	Primary B cells from cord blood	blood
13	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr4:48347000-48354600	Weak transcription	Aorta	Aorta
15	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
16	chr4:48347400-48354600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
18	chr4:48347400-48362200	Weak transcription	NHLF	lung
19	chr4:48347600-48354600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
22	chr4:48348800-48355800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:48348800-48358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
25	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:48349000-48356600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:48349000-48358400	Weak transcription	HSMM	muscle
28	chr4:48349200-48354600	Weak transcription	K562	blood
29	chr4:48349400-48354600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:48349400-48357200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:48349400-48358000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:48349400-48361800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:48349400-48361800	Weak transcription	HMEC	breast
34	chr4:48349400-48362200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:48349600-48354600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr4:48349600-48357000	Weak transcription	Lung	lung
37	chr4:48349600-48363200	Weak transcription	Adipose Nuclei	Adipose
38	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
39	chr4:48350000-48358600	Weak transcription	Ovary	ovary
40	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:48350400-48355400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr4:48350600-48354600	Weak transcription	Right Ventricle	heart
43	chr4:48350600-48355800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr4:48351000-48354200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr4:48351400-48354600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:48351400-48354600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:48351400-48361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:48351400-48362600	Weak transcription	A549	lung
49	chr4:48351600-48355200	Weak transcription	HepG2	liver
50	chr4:48352000-48354400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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