Variant report

Variant	rs942292
Chromosome Location	chr9:110076032-110076033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110044399..110049612-chr9:110071012..110080286,12	K562	blood:
2	chr9:110042843..110044728-chr9:110074492..110076234,2	K562	blood:
3	chr9:110069222..110072456-chr9:110073619..110076462,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10521083	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10732368	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739232	0.81[CHB][hapmap]
rs10739234	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739236	0.85[CHD][hapmap]
rs10739237	0.87[ASN][1000 genomes]
rs10739238	0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs10759222	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759223	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759225	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759226	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759227	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816475	0.89[CHB][hapmap]
rs10816486	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816487	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816492	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816493	0.94[ASN][1000 genomes]
rs10978767	0.83[CHB][hapmap]
rs10978798	0.93[ASN][1000 genomes]
rs11573709	0.85[LWK][hapmap];0.86[YRI][hapmap]
rs1323806	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs1323808	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323809	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1408135	0.89[CHB][hapmap]
rs1535765	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805332	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1805334	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1805335	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886134	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1969798	0.90[ASN][1000 genomes]
rs1980725	0.91[ASN][1000 genomes]
rs2147071	0.91[ASN][1000 genomes]
rs2147072	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2417783	0.84[ASN][1000 genomes]
rs2417784	0.88[CHD][hapmap]
rs2417785	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818367	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4278207	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4625087	0.89[ASN][1000 genomes]
rs4978404	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4978406	0.94[ASN][1000 genomes]
rs4978764	0.89[CHB][hapmap]
rs4978844	0.94[ASN][1000 genomes]
rs4978849	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs698475	0.88[CHD][hapmap]
rs7019341	0.92[ASN][1000 genomes]
rs7025563	0.87[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7029997	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030169	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030555	0.91[ASN][1000 genomes]
rs7030631	0.91[ASN][1000 genomes]
rs7031906	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7035611	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7035725	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7038737	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7039041	0.91[ASN][1000 genomes]
rs7041137	0.85[CHD][hapmap]
rs7041497	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7043962	0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7046950	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7856112	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856227	0.94[ASN][1000 genomes]
rs7859769	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867544	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs817836	0.88[CHD][hapmap]
rs817840	0.85[CHD][hapmap]
rs817841	0.85[CHD][hapmap]
rs942293	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs942292	RAD23B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:110057200-110079200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
4	chr9:110061400-110094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:110062000-110078000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:110062400-110077800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:110062400-110078600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:110062600-110078800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr9:110062800-110077600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:110063000-110077200	Strong transcription	A549	lung
11	chr9:110063000-110078200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr9:110063000-110079200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:110063200-110077400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:110063200-110077400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr9:110063200-110077800	Strong transcription	Placenta	Placenta
16	chr9:110063400-110077800	Strong transcription	Fetal Lung	lung
17	chr9:110063600-110078600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:110063800-110079200	Strong transcription	Osteobl	bone
19	chr9:110063800-110079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:110064000-110085000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:110065200-110089200	Strong transcription	Fetal Thymus	thymus
22	chr9:110065400-110077800	Strong transcription	Primary B cells from cord blood	blood
23	chr9:110065600-110098600	Strong transcription	Dnd41	blood
24	chr9:110067000-110077800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr9:110067400-110076600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:110068400-110077200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr9:110068600-110077400	Strong transcription	HUVEC	blood vessel
28	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr9:110070400-110085000	Weak transcription	Colonic Mucosa	Colon
30	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:110070600-110079400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:110071400-110077600	Strong transcription	HepG2	liver
33	chr9:110071400-110084000	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
35	chr9:110071800-110076400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:110071800-110079800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:110071800-110084400	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:110072600-110076200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr9:110072600-110076400	Strong transcription	Hela-S3	cervix
40	chr9:110072600-110077800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:110072800-110076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:110072800-110077200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:110072800-110077800	Strong transcription	Liver	Liver
44	chr9:110072800-110078400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:110073000-110077000	Strong transcription	NH-A	brain
46	chr9:110073800-110080000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:110074000-110076400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr9:110074000-110076800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:110074000-110076800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:110074000-110077400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links