Variant report

Variant	rs12602583
Chromosome Location	chr17:17091799-17091800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17091463-17092210	K562	blood:	n/a	n/a
2	POLR2A	chr17:17091215-17091866	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17090881..17093719-chr17:17108293..17110165,2	K562	blood:
2	chr17:17084528..17086994-chr17:17091747..17094642,2	K562	blood:
3	chr17:17091439..17092954-chr17:17102481..17104887,2	K562	blood:
4	chr17:17089905..17092856-chr17:17094714..17097551,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf84-1	chr17:17087243-17091977	predAs_engstrom06_CD171782_1

No data

Variant related genes	Relation type
ENSG00000263624	TF binding region
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1047799	0.95[ASN][1000 genomes]
rs1047805	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852844	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10852846	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11078368	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11078371	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11078372	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078373	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1110505	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11551189	0.91[ASN][1000 genomes]
rs11651938	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11652678	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11654887	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11657189	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870035	0.90[ASN][1000 genomes]
rs11870483	0.80[ASN][1000 genomes]
rs12451343	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12452303	0.80[AMR][1000 genomes]
rs12602124	0.80[AMR][1000 genomes]
rs12602592	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602839	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12603417	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1567815	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17794784	0.94[ASN][1000 genomes]
rs2292526	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292530	0.94[ASN][1000 genomes]
rs2349645	0.90[ASN][1000 genomes]
rs2349648	0.80[ASN][1000 genomes]
rs34976658	0.98[ASN][1000 genomes]
rs3744125	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744127	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744131	0.91[ASN][1000 genomes]
rs3744132	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744134	0.90[ASN][1000 genomes]
rs3744136	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3744137	0.90[ASN][1000 genomes]
rs3744138	0.90[ASN][1000 genomes]
rs3744139	0.90[ASN][1000 genomes]
rs3826305	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073688	0.83[EUR][1000 genomes]
rs4073940	0.80[AMR][1000 genomes]
rs4074612	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4074819	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4283273	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321246	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4629023	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985703	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985704	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4985715	0.80[AMR][1000 genomes]
rs4985716	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4985723	0.80[AMR][1000 genomes]
rs4985728	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985730	0.80[ASN][1000 genomes]
rs4985737	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985741	0.98[ASN][1000 genomes]
rs4985742	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985743	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985745	0.94[ASN][1000 genomes]
rs56133536	0.90[ASN][1000 genomes]
rs58326998	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59394251	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60128647	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7211576	0.98[ASN][1000 genomes]
rs7212275	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7214429	0.91[ASN][1000 genomes]
rs7216677	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7223924	0.80[AMR][1000 genomes]
rs73979060	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73979078	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8066111	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8066234	0.94[ASN][1000 genomes]
rs8069259	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8071254	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8077360	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9893676	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9895060	0.85[ASN][1000 genomes]
rs9897510	0.91[ASN][1000 genomes]
rs9910857	0.90[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	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12602583	M-RIP	Cis_1M	lymphoblastoid	RTeQTL
rs12602583	LOC201164	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
2	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
3	chr17:17051000-17093200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:17055600-17092600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:17055800-17092600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr17:17056000-17093600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:17056200-17092400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr17:17056600-17093600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:17056800-17095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:17060400-17093400	Strong transcription	Liver	Liver
11	chr17:17060800-17093600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:17067800-17092200	Strong transcription	Brain Cingulate Gyrus	brain
13	chr17:17076200-17092600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:17076200-17094600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr17:17076600-17104600	Weak transcription	K562	blood
16	chr17:17083600-17093200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr17:17084200-17092400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr17:17084400-17093400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr17:17084400-17095200	Weak transcription	Fetal Kidney	kidney
20	chr17:17084800-17094800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:17084800-17094800	Weak transcription	Fetal Brain Male	brain
22	chr17:17085600-17094800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:17086400-17095200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr17:17086400-17104800	Weak transcription	Brain Substantia Nigra	brain
25	chr17:17086400-17106600	Weak transcription	Colonic Mucosa	Colon
26	chr17:17086600-17093000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr17:17086600-17094800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:17087000-17092800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:17087200-17094800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr17:17087600-17092800	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:17087600-17093800	Enhancers	Fetal Heart	heart
32	chr17:17087600-17093800	Genic enhancers	HSMMtube	muscle
33	chr17:17087600-17095400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:17087800-17093200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:17087800-17093800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr17:17087800-17094800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr17:17088000-17093600	Weak transcription	NHDF-Ad	bronchial
38	chr17:17088000-17093800	Genic enhancers	Placenta	Placenta
39	chr17:17088000-17094000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr17:17088200-17093000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr17:17088200-17093400	Weak transcription	Psoas Muscle	Psoas
42	chr17:17088200-17093800	Weak transcription	Brain Anterior Caudate	brain
43	chr17:17088400-17093600	Strong transcription	Thymus	Thymus
44	chr17:17088600-17093000	Weak transcription	Right Atrium	heart
45	chr17:17088800-17093000	Weak transcription	Aorta	Aorta
46	chr17:17088800-17093400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr17:17089000-17092400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr17:17089200-17091800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr17:17089200-17093800	Genic enhancers	HMEC	breast
50	chr17:17089400-17093600	Strong transcription	Dnd41	blood

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