Variant report

Variant	rs2090018
Chromosome Location	chr17:17020967-17020968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17010273..17011801-chr17:17020537..17022736,2	K562	blood:
2	chr17:17011485..17013573-chr17:17019778..17021863,2	MCF-7	breast:
3	chr17:17020278..17022879-chr17:17024939..17027865,2	K562	blood:
4	chr17:17014931..17017643-chr17:17019821..17021328,2	K562	blood:
5	chr17:16991616..16993705-chr17:17019243..17022141,2	MCF-7	breast:
6	chr17:17008907..17011801-chr17:17020811..17022736,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11078374	1.00[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11656868	1.00[CHB][hapmap]
rs11871902	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349646	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28461224	1.00[ASN][1000 genomes]
rs4247118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247120	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4275914	1.00[ASN][1000 genomes]
rs4514740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985696	1.00[ASN][1000 genomes]
rs4985701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985717	1.00[ASN][1000 genomes]
rs4985718	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4985740	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4985746	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6502563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206981	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7208929	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7208973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217091	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220827	1.00[CHB][hapmap]
rs7221842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7222311	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064550	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072184	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8073842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8079563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9893911	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9898995	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908767	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914671	1.00[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	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv984510	chr17:17015688-17048858	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2090018	RNF112	cis	cerebellum	SCAN
rs2090018	FLCN	cis	cerebellum	SCAN
rs2090018	ULK2	cis	cerebellum	SCAN
rs2090018	TOM1L2	cis	cerebellum	SCAN
rs2090018	M-RIP	cis	multi-tissue	Pritchard
rs2090018	UBB	cis	cerebellum	SCAN
rs2090018	FLCN	cis	parietal	SCAN
rs2090018	TRPV2	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17002600-17023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:17006200-17033000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:17007800-17021000	Weak transcription	HepG2	liver
4	chr17:17009200-17025200	Enhancers	Brain Anterior Caudate	brain
5	chr17:17010000-17032000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:17010200-17021600	Weak transcription	Dnd41	blood
7	chr17:17010200-17025000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr17:17010200-17025000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:17010400-17024000	Enhancers	Primary B cells from peripheral blood	blood
10	chr17:17010400-17025200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:17011200-17028800	Weak transcription	Fetal Brain Female	brain
12	chr17:17011400-17021600	Weak transcription	Aorta	Aorta
13	chr17:17012000-17035200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:17012600-17023600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:17014000-17022200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr17:17015400-17035200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:17015800-17023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:17015800-17025200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr17:17015800-17030000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:17016400-17022400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:17016400-17025000	Enhancers	Brain Substantia Nigra	brain
22	chr17:17016800-17025400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr17:17017600-17022200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr17:17017600-17025000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr17:17017600-17025000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr17:17017600-17025000	Enhancers	Brain Hippocampus Middle	brain
27	chr17:17017600-17025200	Enhancers	Fetal Heart	heart
28	chr17:17017800-17021800	Enhancers	Gastric	stomach
29	chr17:17017800-17025000	Enhancers	Left Ventricle	heart
30	chr17:17017800-17025000	Enhancers	Ovary	ovary
31	chr17:17017800-17025000	Enhancers	Right Atrium	heart
32	chr17:17017800-17025000	Enhancers	Right Ventricle	heart
33	chr17:17017800-17025000	Enhancers	Spleen	Spleen
34	chr17:17018000-17022800	Weak transcription	Fetal Kidney	kidney
35	chr17:17018000-17025000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:17018000-17025000	Genic enhancers	Fetal Intestine Small	intestine
37	chr17:17018000-17025000	Enhancers	Pancreas	Pancrea
38	chr17:17018400-17024400	Genic enhancers	Fetal Stomach	stomach
39	chr17:17018600-17021600	Weak transcription	NH-A	brain
40	chr17:17018600-17022000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr17:17018800-17021400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:17018800-17021400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:17018800-17021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:17018800-17021800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:17018800-17021800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr17:17018800-17021800	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr17:17018800-17021800	Weak transcription	Osteobl	bone
48	chr17:17018800-17022000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr17:17018800-17023400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr17:17018800-17025000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links