Variant report

Variant	rs10076
Chromosome Location	chr13:49079503-49079504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49075530..49077233-chr13:49077933..49080570,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10467381	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11840819	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11842402	0.95[AMR][1000 genomes]
rs11842662	0.90[AMR][1000 genomes]
rs13378245	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17071695	1.00[CHD][hapmap]
rs17071917	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17071960	0.90[AMR][1000 genomes]
rs174854	0.90[AMR][1000 genomes]
rs174858	1.00[CHD][hapmap]
rs198565	0.90[AMR][1000 genomes]
rs198573	0.90[AMR][1000 genomes]
rs198581	0.85[AMR][1000 genomes]
rs198583	0.90[AMR][1000 genomes]
rs198587	0.90[AMR][1000 genomes]
rs198617	1.00[CHD][hapmap]
rs198618	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2804082	0.82[ASW][hapmap]
rs2804085	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2804088	0.82[MEX][hapmap]
rs2804091	0.82[MEX][hapmap]
rs2854361	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs2984828	0.90[AMR][1000 genomes]
rs3020646	1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs411862	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs4151590	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs449268	1.00[CHD][hapmap]
rs7322110	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7332631	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7984270	0.95[AMR][1000 genomes]
rs9316384	0.86[AMR][1000 genomes]
rs9316386	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9316387	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9316390	0.89[EUR][1000 genomes]
rs9316391	0.89[EUR][1000 genomes]
rs9316392	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[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]
rs9316396	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9316403	0.95[AMR][1000 genomes]
rs9332025	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9332036	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9332050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9332053	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes]
rs9332066	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs9591167	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9591170	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9591171	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9591174	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9591175	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9595894	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9595913	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595914	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9595917	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9595930	0.90[AMR][1000 genomes]
rs9595936	0.90[AMR][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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10076	RCBTB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49054000-49094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:49063000-49087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:49066800-49080200	Weak transcription	Colonic Mucosa	Colon
4	chr13:49067000-49080200	Weak transcription	Psoas Muscle	Psoas
5	chr13:49067000-49084200	Weak transcription	Ovary	ovary
6	chr13:49067200-49079600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr13:49067200-49080200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr13:49067200-49105200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr13:49067200-49105400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:49067800-49098000	Weak transcription	Right Ventricle	heart
11	chr13:49068000-49105600	Weak transcription	Gastric	stomach
12	chr13:49068200-49102600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr13:49068400-49081000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr13:49071200-49105600	Weak transcription	Fetal Brain Male	brain
15	chr13:49071800-49086200	Strong transcription	Fetal Stomach	stomach
16	chr13:49071800-49105800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr13:49072000-49088400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr13:49072200-49080200	Weak transcription	Spleen	Spleen
19	chr13:49072200-49085800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:49072200-49095600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:49072400-49079800	Weak transcription	Brain Substantia Nigra	brain
22	chr13:49072400-49080200	Weak transcription	Aorta	Aorta
23	chr13:49072400-49080400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:49073200-49085800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:49073400-49080200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:49073600-49087800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:49073800-49081200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr13:49074200-49079600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr13:49074800-49083000	Weak transcription	Fetal Intestine Small	intestine
30	chr13:49075400-49080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:49075400-49085800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr13:49075600-49093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr13:49075600-49095200	Weak transcription	Fetal Intestine Large	intestine
34	chr13:49075800-49080200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:49075800-49080400	Weak transcription	NHLF	lung
36	chr13:49075800-49086000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:49075800-49088400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:49075800-49093200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:49076000-49080000	Weak transcription	Brain Anterior Caudate	brain
40	chr13:49076000-49083000	Weak transcription	Fetal Lung	lung
41	chr13:49076000-49084800	Weak transcription	Liver	Liver
42	chr13:49076000-49085800	Weak transcription	Fetal Kidney	kidney
43	chr13:49076600-49084800	Weak transcription	Brain Germinal Matrix	brain
44	chr13:49076600-49097400	Weak transcription	Pancreas	Pancrea
45	chr13:49077000-49085800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:49077200-49079600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:49077200-49080000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr13:49077400-49079600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr13:49077400-49080600	Weak transcription	Fetal Brain Female	brain
50	chr13:49077600-49079600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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