Variant report

Variant	rs17086588
Chromosome Location	chr5:96044914-96044915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96044782..96047336-chr5:96048549..96051619,3	K562	blood:
2	chr5:96036755..96041395-chr5:96042282..96045652,7	K562	blood:
3	chr5:96037082..96041395-chr5:96043344..96047377,11	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10447215	0.85[EUR][1000 genomes]
rs10515244	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs11738135	1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739280	0.85[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11745122	0.85[EUR][1000 genomes]
rs11748795	0.91[MEX][hapmap]
rs11750399	0.85[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11750400	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs11750510	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12188168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559085	0.85[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs17082200	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400685	0.85[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs17400741	0.85[EUR][1000 genomes]
rs17479052	0.85[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2112277	1.00[ASN][1000 genomes]
rs34942552	0.98[EUR][1000 genomes]
rs4869305	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs55695458	0.99[EUR][1000 genomes]
rs56116814	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56122780	0.85[EUR][1000 genomes]
rs56257788	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6879175	1.00[ASN][1000 genomes]
rs72772090	0.99[EUR][1000 genomes]
rs72772091	1.00[EUR][1000 genomes]
rs72772092	1.00[EUR][1000 genomes]
rs72772095	0.98[EUR][1000 genomes]
rs73774355	1.00[ASN][1000 genomes]
rs7702304	0.81[ASW][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]

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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17086588	CAST	cis	parietal	SCAN
rs17086588	C5orf36	cis	cerebellum	SCAN
rs17086588	ERAP1	cis	parietal	SCAN
rs17086588	CAST	cis	cerebellum	SCAN
rs17086588	CAST	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96039200-96050600	Weak transcription	Gastric	stomach
2	chr5:96039200-96054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:96039200-96054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:96039200-96054400	Weak transcription	Spleen	Spleen
5	chr5:96039200-96059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:96039400-96050200	Weak transcription	Aorta	Aorta
7	chr5:96039600-96046200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:96039600-96063600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:96039800-96048000	Weak transcription	Pancreas	Pancrea
10	chr5:96039800-96049600	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:96039800-96049800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:96040000-96046000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr5:96040000-96046600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:96040000-96047400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:96040000-96049600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:96040000-96049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:96040000-96050000	Weak transcription	Primary T cells from cord blood	blood
18	chr5:96040000-96050000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:96040000-96050200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:96040000-96050400	Weak transcription	Primary B cells from cord blood	blood
21	chr5:96040000-96054400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:96040000-96054400	Weak transcription	Fetal Stomach	stomach
23	chr5:96040200-96046600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:96040200-96046800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:96040200-96049400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:96040200-96049800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:96040200-96050200	Weak transcription	Brain Substantia Nigra	brain
28	chr5:96040200-96050600	Weak transcription	Brain Anterior Caudate	brain
29	chr5:96040400-96047200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:96040400-96049800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:96040600-96046800	Weak transcription	Liver	Liver
32	chr5:96040600-96047400	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:96040600-96048600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:96040600-96050200	Weak transcription	Fetal Kidney	kidney
35	chr5:96041000-96046800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:96041000-96048600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:96041600-96046200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:96041600-96054600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:96041800-96045600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:96041800-96049600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:96042000-96045000	Enhancers	Fetal Intestine Large	intestine
42	chr5:96042000-96045400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr5:96042200-96045000	Enhancers	Left Ventricle	heart
44	chr5:96042200-96045400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:96042200-96045400	Enhancers	Stomach Mucosa	stomach
46	chr5:96042200-96045800	Enhancers	Fetal Heart	heart
47	chr5:96042600-96046600	Weak transcription	HepG2	liver
48	chr5:96042800-96046000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr5:96042800-96046000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood

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