Variant report

Variant	rs11163983
Chromosome Location	chr1:84955233-84955234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84954216..84956546-chr1:84965976..84968272,2	MCF-7	breast:
2	chr1:84942484..84947798-chr1:84954955..84960241,6	MCF-7	breast:
3	chr1:84953201..84955322-chr1:85035250..85039258,3	K562	blood:

Variant related genes	Relation type
ENSG00000117133	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10874450	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11163977	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11163978	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11163984	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11163989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11163995	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11163997	1.00[EUR][1000 genomes]
rs11163998	1.00[YRI][hapmap]
rs12067077	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075688	0.85[ASW][hapmap];1.00[YRI][hapmap]
rs12077012	1.00[EUR][1000 genomes]
rs12092954	0.82[EUR][1000 genomes]
rs12093101	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12125825	1.00[CEU][hapmap]
rs12129197	1.00[CEU][hapmap]
rs12134893	0.95[EUR][1000 genomes]
rs12137560	0.95[EUR][1000 genomes]
rs12141175	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12144912	0.95[EUR][1000 genomes]
rs1803276	0.85[ASW][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11163983	RPF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84946000-84956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:84946000-84956400	Weak transcription	Gastric	stomach
3	chr1:84946000-84956400	Weak transcription	Spleen	Spleen
4	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
7	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:84946200-84956200	Weak transcription	Colonic Mucosa	Colon
10	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
11	chr1:84946400-84955600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:84946400-84956200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:84946400-84956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:84946400-84962000	Weak transcription	Fetal Brain Male	brain
15	chr1:84946400-84962800	Weak transcription	Stomach Mucosa	stomach
16	chr1:84946600-84955600	Weak transcription	Brain Germinal Matrix	brain
17	chr1:84946600-84956400	Weak transcription	Psoas Muscle	Psoas
18	chr1:84946800-84955400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:84946800-84967400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:84947000-84965800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:84947200-84955400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:84947200-84955600	Weak transcription	Pancreas	Pancrea
23	chr1:84947200-84955600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:84947200-84956400	Weak transcription	Brain Angular Gyrus	brain
25	chr1:84947200-84956400	Weak transcription	NHLF	lung
26	chr1:84947200-84958400	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:84947400-84955800	Weak transcription	HMEC	breast
28	chr1:84947400-84957200	Weak transcription	Fetal Heart	heart
29	chr1:84947400-84957600	Weak transcription	Lung	lung
30	chr1:84947400-84969800	Weak transcription	Aorta	Aorta
31	chr1:84947800-84966000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:84947800-84967800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:84948200-84956400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:84949600-84968400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:84949800-84955600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:84949800-84962000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:84950000-84955600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:84951200-84956200	Weak transcription	Fetal Stomach	stomach
39	chr1:84951200-84956400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:84951200-84971000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:84951400-84955600	Weak transcription	Brain Anterior Caudate	brain
42	chr1:84951400-84956400	Weak transcription	Fetal Intestine Small	intestine
43	chr1:84951400-84956400	Weak transcription	Left Ventricle	heart
44	chr1:84951600-84955600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:84951800-84956200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:84952000-84955400	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:84952000-84955600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:84952000-84955600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:84952400-84967400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:84953800-84968400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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