Variant report

Variant	rs563798
Chromosome Location	chr10:6552852-6552853
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	chr10:6542478..6544249-chr10:6551947..6554628,2	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2387407	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs500766	0.85[JPT][hapmap]
rs510745	1.00[ASW][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes]
rs586355	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs606289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs667254	0.85[JPT][hapmap]
rs676674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7083579	1.00[ASW][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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5687	chr10:6537209-6556751	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs563798	FBXO18	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
2	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:6518200-6556800	Weak transcription	Fetal Intestine Large	intestine
6	chr10:6526600-6553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:6535400-6553400	Weak transcription	Gastric	stomach
8	chr10:6540800-6556600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:6541600-6555200	Strong transcription	Primary T cells from cord blood	blood
10	chr10:6542000-6553000	Strong transcription	Fetal Thymus	thymus
11	chr10:6543000-6555000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr10:6543200-6554600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr10:6544600-6553000	Weak transcription	Pancreas	Pancrea
14	chr10:6544600-6558200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr10:6545200-6554800	Weak transcription	Psoas Muscle	Psoas
16	chr10:6546800-6561200	Weak transcription	HMEC	breast
17	chr10:6547200-6554200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr10:6548600-6554800	Strong transcription	Dnd41	blood
19	chr10:6549400-6553200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr10:6549800-6562400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:6550000-6554200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr10:6550400-6553600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:6550400-6562600	Weak transcription	Brain Substantia Nigra	brain
24	chr10:6550600-6554600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr10:6550600-6555400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr10:6550600-6555400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:6550600-6562400	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:6550800-6554200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr10:6550800-6554200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:6550800-6555000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr10:6551200-6554600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:6552000-6553600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:6552000-6553600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr10:6552200-6553200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr10:6552200-6555200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:6552600-6553000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:6552600-6553200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr10:6552600-6553200	Strong transcription	Fetal Kidney	kidney
39	chr10:6552600-6553200	ZNF genes & repeats	K562	blood
40	chr10:6552600-6553400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
41	chr10:6552600-6553600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:6552600-6554600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr10:6552800-6553000	ZNF genes & repeats	Lung	lung
44	chr10:6552800-6553200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:6552800-6553200	Enhancers	Fetal Stomach	stomach
46	chr10:6552800-6553200	ZNF genes & repeats	NHEK	skin
47	chr10:6552800-6553400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr10:6552800-6553400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr10:6552800-6553600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
50	chr10:6552800-6553600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell

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