Variant report

Variant	rs368609
Chromosome Location	chr4:48359761-48359762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48354378..48356261-chr4:48359640..48362289,3	K562	blood:
2	chr4:48351553..48354497-chr4:48357846..48360207,2	MCF-7	breast:
3	chr4:48353391..48356261-chr4:48359560..48361635,3	K562	blood:
4	chr4:48348136..48350109-chr4:48359251..48361101,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1117010	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12507206	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12511991	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12649527	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12649528	0.85[EUR][1000 genomes]
rs13105385	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13115295	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13133788	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13148849	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13150017	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1352433	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2291474	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2353312	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28409655	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs372825	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs382335	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3828496	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs392187	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs403495	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs421336	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs421833	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs432927	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs445892	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs449376	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6447634	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6816352	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6821277	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6837335	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7438704	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7672892	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7674269	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs923372	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs923373	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9291323	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs974014	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs974015	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs974016	0.87[AMR][1000 genomes];0.83[EUR][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
rs368609	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344800-48362400	Weak transcription	Gastric	stomach
2	chr4:48346000-48362800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
5	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
7	chr4:48347400-48362200	Weak transcription	NHLF	lung
8	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
10	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
11	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:48349400-48361800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:48349400-48361800	Weak transcription	HMEC	breast
14	chr4:48349400-48362200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:48349600-48363200	Weak transcription	Adipose Nuclei	Adipose
16	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
17	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:48351400-48361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:48351400-48362600	Weak transcription	A549	lung
20	chr4:48352400-48362200	Weak transcription	Left Ventricle	heart
21	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr4:48353200-48362800	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:48353200-48362800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:48353600-48362200	Weak transcription	Brain Anterior Caudate	brain
26	chr4:48353600-48362200	Weak transcription	Fetal Heart	heart
27	chr4:48353600-48363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:48353800-48362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
30	chr4:48354800-48362200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:48354800-48362400	Weak transcription	Right Ventricle	heart
32	chr4:48355000-48359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:48355000-48361200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:48355000-48361600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:48355000-48361800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:48355000-48362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
38	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:48355000-48412600	Weak transcription	Aorta	Aorta
40	chr4:48355200-48363200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:48355200-48377600	Weak transcription	Fetal Intestine Small	intestine
42	chr4:48355200-48379800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:48355400-48363000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr4:48355400-48371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:48355800-48390600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:48356000-48362800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:48356600-48367800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:48357200-48362200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:48357200-48362400	Weak transcription	Psoas Muscle	Psoas
50	chr4:48357200-48384600	Weak transcription	Lung	lung

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