Variant report

Variant	rs10000288
Chromosome Location	chr4:48357527-48357528
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:
2	chr4:48343973..48346063-chr4:48356828..48359174,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10001054	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10003458	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10004425	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10024547	0.80[ASN][1000 genomes]
rs10517217	0.85[ASN][1000 genomes]
rs1055720	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1055721	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10938530	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11731199	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11737752	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13122065	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13141335	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17655838	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1876834	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28411210	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28464394	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28636546	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28659782	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28690347	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4695376	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447631	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447632	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66894522	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68142816	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6841390	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6843652	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6853315	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655066	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7658851	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7662325	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7688310	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884339	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9992736	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995939	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9999482	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[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
rs10000288	SLAIN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 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	chr4:48346200-48358400	Weak transcription	Small Intestine	intestine
4	chr4:48346200-48362400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:48346400-48361200	Weak transcription	Thymus	Thymus
6	chr4:48346600-48371000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr4:48347200-48359600	Weak transcription	Fetal Stomach	stomach
8	chr4:48347400-48362200	Weak transcription	Brain Substantia Nigra	brain
9	chr4:48347400-48362200	Weak transcription	NHLF	lung
10	chr4:48347600-48365000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:48348600-48362400	Weak transcription	Fetal Lung	lung
12	chr4:48348800-48358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:48348800-48363000	Weak transcription	Hela-S3	cervix
14	chr4:48348800-48371000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:48349000-48358400	Weak transcription	HSMM	muscle
16	chr4:48349400-48358000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:48349400-48361800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:48349400-48361800	Weak transcription	HMEC	breast
19	chr4:48349400-48362200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:48349600-48363200	Weak transcription	Adipose Nuclei	Adipose
21	chr4:48349600-48364400	Weak transcription	Right Atrium	heart
22	chr4:48350000-48358600	Weak transcription	Ovary	ovary
23	chr4:48350000-48375800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr4:48351400-48361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:48351400-48362600	Weak transcription	A549	lung
26	chr4:48352400-48358400	Weak transcription	NHEK	skin
27	chr4:48352400-48362200	Weak transcription	Left Ventricle	heart
28	chr4:48352800-48358200	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:48352800-48372400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:48353000-48371200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:48353200-48362800	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:48353200-48362800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr4:48353600-48358200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:48353600-48358400	Weak transcription	Brain Angular Gyrus	brain
35	chr4:48353600-48362200	Weak transcription	Brain Anterior Caudate	brain
36	chr4:48353600-48362200	Weak transcription	Fetal Heart	heart
37	chr4:48353600-48363200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:48353800-48362400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:48353800-48369200	Weak transcription	Pancreas	Pancrea
40	chr4:48354800-48362200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:48354800-48362400	Weak transcription	Right Ventricle	heart
42	chr4:48355000-48357800	Weak transcription	K562	blood
43	chr4:48355000-48358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:48355000-48359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:48355000-48361200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:48355000-48361600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:48355000-48361800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:48355000-48362400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:48355000-48376600	Weak transcription	Primary B cells from cord blood	blood
50	chr4:48355000-48380000	Weak transcription	Primary T cells fromperipheralblood	blood

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