Variant report

Variant	rs2291475
Chromosome Location	chr4:48380480-48380481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:48380383-48380520	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48341542..48343650-chr4:48378558..48381453,2	K562	blood:

Variant related genes	Relation type
SLAIN2	TF binding region
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10003230	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10026398	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10029785	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10805168	0.89[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs1117010	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11945562	0.86[JPT][hapmap]
rs12503644	0.85[ASN][1000 genomes]
rs12507206	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511991	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12645951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649527	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649528	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13105385	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13115295	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13133788	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13148849	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13150017	0.86[EUR][1000 genomes]
rs1352433	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1352434	0.88[ASN][1000 genomes]
rs1472967	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1507865	0.81[JPT][hapmap]
rs1586540	0.92[ASN][1000 genomes]
rs1703973	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1948167	0.92[ASN][1000 genomes]
rs2029348	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291474	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2353312	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353314	0.88[ASN][1000 genomes]
rs2353315	0.82[ASN][1000 genomes]
rs28409655	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34975258	0.82[ASN][1000 genomes]
rs35758434	0.92[ASN][1000 genomes]
rs372825	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs382335	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3828496	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs392187	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs404348	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404445	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs404656	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs411261	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]
rs421336	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs421833	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs429969	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs432927	0.84[EUR][1000 genomes]
rs445892	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs449376	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs450498	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4536901	0.81[JPT][hapmap]
rs4694895	0.92[ASN][1000 genomes]
rs62309425	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447634	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447635	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816010	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816352	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821277	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829705	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6844211	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848395	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7438704	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7668529	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7672892	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7674269	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7678164	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs923372	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs923373	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9291323	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs974014	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974015	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974016	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs992423	0.86[JPT][hapmap]
rs9996532	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2291475	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
2	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:48357200-48384600	Weak transcription	Lung	lung
4	chr4:48359200-48384400	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:48361000-48384600	Weak transcription	Fetal Stomach	stomach
6	chr4:48362600-48384600	Weak transcription	Left Ventricle	heart
7	chr4:48363000-48384600	Weak transcription	Ovary	ovary
8	chr4:48363400-48405400	Weak transcription	Right Ventricle	heart
9	chr4:48363600-48382600	Weak transcription	Fetal Brain Male	brain
10	chr4:48363600-48382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:48364000-48381400	Weak transcription	Fetal Heart	heart
12	chr4:48364200-48381800	Weak transcription	Adipose Nuclei	Adipose
13	chr4:48368600-48384600	Weak transcription	Thymus	Thymus
14	chr4:48368800-48384600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:48369600-48382600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:48371400-48395400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:48372000-48380600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:48372000-48384200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:48372200-48380800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:48372600-48387000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:48372600-48426800	Weak transcription	Small Intestine	intestine
22	chr4:48372800-48380600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:48372800-48381000	Weak transcription	Fetal Brain Female	brain
24	chr4:48372800-48381400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:48372800-48381800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:48372800-48382000	Weak transcription	GM12878-XiMat	blood
27	chr4:48372800-48382600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:48372800-48384600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:48373000-48380600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:48373000-48381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:48373000-48381600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:48373000-48381600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:48373000-48384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:48373000-48384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:48373200-48381800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:48374000-48382000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:48374000-48383000	Weak transcription	Fetal Thymus	thymus
38	chr4:48374000-48384600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:48374000-48385600	Weak transcription	Right Atrium	heart
40	chr4:48374600-48382400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:48375400-48381800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:48375400-48382200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr4:48375600-48382000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:48375800-48384600	Weak transcription	K562	blood
45	chr4:48376200-48382000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:48377800-48384600	Weak transcription	Pancreas	Pancrea
47	chr4:48377800-48405000	Weak transcription	Esophagus	oesophagus
48	chr4:48377800-48423800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:48378000-48382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr4:48378000-48384600	Weak transcription	Fetal Kidney	kidney

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