Variant report

Variant	rs17472113
Chromosome Location	chr4:48495662-48495663
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48478067..48481410-chr4:48493413..48496125,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10031120	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10517217	0.80[JPT][hapmap]
rs1055721	0.85[JPT][hapmap]
rs13125511	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1996422	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4413478	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6447631	0.85[JPT][hapmap]
rs6812622	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6827019	0.86[ASN][1000 genomes]
rs7340880	0.88[ASN][1000 genomes]
rs7655066	0.85[JPT][hapmap]
rs7664981	0.94[JPT][hapmap]
rs7668401	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7688310	0.85[JPT][hapmap]
rs7694862	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992736	0.85[JPT][hapmap]
rs9993088	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9999482	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17472113	SLAIN2	cis	cerebellum	SCAN
rs17472113	SLAIN2	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48487200-48505800	Weak transcription	A549	lung
2	chr4:48492400-48500800	Weak transcription	Brain Substantia Nigra	brain
3	chr4:48492600-48497800	Weak transcription	Aorta	Aorta
4	chr4:48492600-48510600	Weak transcription	HepG2	liver
5	chr4:48492800-48500200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:48492800-48500800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:48493600-48498000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:48493600-48500800	Weak transcription	Left Ventricle	heart
9	chr4:48493600-48509200	Weak transcription	Pancreas	Pancrea
10	chr4:48493600-48510600	Weak transcription	Gastric	stomach
11	chr4:48493600-48523000	Weak transcription	Right Ventricle	heart
12	chr4:48493800-48498000	Weak transcription	HSMM	muscle
13	chr4:48493800-48499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:48493800-48500800	Weak transcription	Ovary	ovary
15	chr4:48493800-48502800	Weak transcription	Spleen	Spleen
16	chr4:48493800-48509600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:48493800-48510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:48494000-48499000	Weak transcription	Placenta	Placenta
19	chr4:48494000-48511600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:48494000-48511800	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:48494200-48496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:48494200-48497400	Weak transcription	Lung	lung
23	chr4:48494200-48498200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:48494200-48499800	Weak transcription	Adipose Nuclei	Adipose
25	chr4:48494200-48499800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:48494200-48500200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr4:48494200-48500800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:48494200-48509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:48494200-48510600	Weak transcription	HSMMtube	muscle
30	chr4:48494400-48497600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:48494400-48498600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:48494600-48499800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:48494600-48500400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:48494600-48501000	Weak transcription	Brain Anterior Caudate	brain
35	chr4:48494800-48499400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:48494800-48500200	Weak transcription	GM12878-XiMat	blood
37	chr4:48494800-48500800	Weak transcription	Brain Angular Gyrus	brain
38	chr4:48494800-48509400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:48494800-48510600	Weak transcription	Esophagus	oesophagus
40	chr4:48495000-48495800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:48495000-48499600	Weak transcription	Primary T cells from cord blood	blood
42	chr4:48495000-48499800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:48495000-48499800	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:48495000-48499800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:48495000-48501400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:48495000-48510000	Weak transcription	Brain Germinal Matrix	brain
47	chr4:48495200-48498000	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:48495200-48500000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:48495200-48500000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr4:48495200-48500200	Weak transcription	Liver	Liver

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