Variant report

Variant	rs9993088
Chromosome Location	chr4:48494546-48494547
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48492886..48494734-chr4:48535449..48537970,2	K562	blood:
2	chr4:48489612..48492154-chr4:48493154..48495602,2	K562	blood:
3	chr4:48478067..48481410-chr4:48493413..48496125,3	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10031120	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10517217	0.80[JPT][hapmap]
rs1055721	0.85[JPT][hapmap]
rs10938532	0.86[AMR][1000 genomes]
rs13125511	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17472113	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996422	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs4413478	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447631	0.85[JPT][hapmap]
rs6812622	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6827019	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7340880	0.90[ASN][1000 genomes]
rs7655066	0.85[JPT][hapmap]
rs7664981	0.94[JPT][hapmap]
rs7668401	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688310	0.85[JPT][hapmap]
rs7694862	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9992736	0.85[JPT][hapmap]
rs9999482	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS 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
rs9993088	SLAIN2	cis	cerebellum	SCAN
rs9993088	SLAIN2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48487200-48505800	Weak transcription	A549	lung
2	chr4:48491400-48495400	Weak transcription	K562	blood
3	chr4:48492400-48500800	Weak transcription	Brain Substantia Nigra	brain
4	chr4:48492600-48497800	Weak transcription	Aorta	Aorta
5	chr4:48492600-48510600	Weak transcription	HepG2	liver
6	chr4:48492800-48500200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:48492800-48500800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:48493600-48498000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:48493600-48500800	Weak transcription	Left Ventricle	heart
10	chr4:48493600-48509200	Weak transcription	Pancreas	Pancrea
11	chr4:48493600-48510600	Weak transcription	Gastric	stomach
12	chr4:48493600-48523000	Weak transcription	Right Ventricle	heart
13	chr4:48493800-48498000	Weak transcription	HSMM	muscle
14	chr4:48493800-48499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:48493800-48500800	Weak transcription	Ovary	ovary
16	chr4:48493800-48502800	Weak transcription	Spleen	Spleen
17	chr4:48493800-48509600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:48493800-48510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:48494000-48499000	Weak transcription	Placenta	Placenta
20	chr4:48494000-48511600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:48494000-48511800	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:48494200-48496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:48494200-48497400	Weak transcription	Lung	lung
24	chr4:48494200-48498200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:48494200-48499800	Weak transcription	Adipose Nuclei	Adipose
26	chr4:48494200-48499800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:48494200-48500200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:48494200-48500800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:48494200-48509800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:48494200-48510600	Weak transcription	HSMMtube	muscle
31	chr4:48494400-48494600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr4:48494400-48497600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:48494400-48498600	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links