Variant report

Variant	rs2417785
Chromosome Location	chr9:110097414-110097415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:110044860..110047881-chr9:110095955..110100656,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10113916	0.84[CHB][hapmap]
rs10119641	0.84[CHB][hapmap]
rs10481632	0.84[CHB][hapmap]
rs10521083	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10732368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739232	0.87[CHB][hapmap]
rs10739234	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739237	0.87[ASN][1000 genomes]
rs10739238	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10759219	0.83[CHB][hapmap]
rs10759222	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759223	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759225	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759226	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759227	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816475	0.95[CHB][hapmap]
rs10816477	0.84[CHB][hapmap]
rs10816485	0.84[CHB][hapmap]
rs10816486	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816487	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816492	0.94[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816493	0.94[ASN][1000 genomes]
rs10978767	0.89[CHB][hapmap]
rs10978769	0.83[CHB][hapmap]
rs10978770	0.83[CHB][hapmap]
rs10978775	0.84[CHB][hapmap]
rs10978791	0.84[CHB][hapmap]
rs10978798	0.93[ASN][1000 genomes]
rs11573709	0.86[YRI][hapmap]
rs12345455	0.84[CHB][hapmap]
rs1323806	0.90[CHB][hapmap]
rs1323808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323809	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1408135	0.95[CHB][hapmap]
rs1535765	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1535766	0.83[CHB][hapmap]
rs1805329	0.84[CHB][hapmap]
rs1805332	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1805334	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1805335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886134	1.00[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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2417783	0.84[ASN][1000 genomes]
rs2417784	0.84[CHB][hapmap]
rs3818367	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4278207	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4625087	0.89[ASN][1000 genomes]
rs4978404	0.81[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4978406	0.94[ASN][1000 genomes]
rs4978764	0.95[CHB][hapmap]
rs4978844	0.94[ASN][1000 genomes]
rs4978849	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs698475	0.84[CHB][hapmap]
rs7019341	0.92[ASN][1000 genomes]
rs7025563	0.82[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7029997	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030169	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030555	0.91[ASN][1000 genomes]
rs7030631	0.91[ASN][1000 genomes]
rs7031906	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7035611	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7035725	0.81[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	0.83[CHB][hapmap]
rs7041497	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7043962	0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7046950	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7852295	0.83[CHB][hapmap]
rs7856112	0.90[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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866312	0.83[CHB][hapmap]
rs7866353	0.84[CHB][hapmap]
rs7866797	0.83[CHB][hapmap]
rs7867544	0.89[CHB][hapmap]
rs817836	0.84[CHB][hapmap]
rs817840	0.84[CHB][hapmap]
rs817841	0.84[CHB][hapmap]
rs942291	0.84[CHB][hapmap]
rs942292	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]
rs942293	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9969728	0.84[CHB][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2417785	RAD23B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
2	chr9:110065600-110098600	Strong transcription	Dnd41	blood
3	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
6	chr9:110079600-110098800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:110079800-110097600	Strong transcription	HSMM	muscle
8	chr9:110079800-110098000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:110080600-110097800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:110084000-110097800	Strong transcription	Hela-S3	cervix
11	chr9:110084800-110098800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:110085400-110097800	Strong transcription	Liver	Liver
13	chr9:110086200-110097600	Strong transcription	NHLF	lung
14	chr9:110087200-110098600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr9:110087600-110103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:110088400-110098800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:110088400-110101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:110088600-110098200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:110088600-110098400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:110088600-110098600	Weak transcription	Fetal Brain Male	brain
23	chr9:110088600-110101600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:110089600-110097800	Strong transcription	Osteobl	bone
25	chr9:110089600-110098000	Strong transcription	K562	blood
26	chr9:110089800-110099400	Strong transcription	Placenta	Placenta
27	chr9:110090200-110097600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr9:110090200-110097600	Strong transcription	Fetal Thymus	thymus
29	chr9:110090200-110097800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:110090400-110098600	Strong transcription	Fetal Muscle Leg	muscle
31	chr9:110090400-110098600	Strong transcription	HUVEC	blood vessel
32	chr9:110090400-110101800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:110090600-110097600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr9:110090600-110097800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:110090600-110097800	Strong transcription	Fetal Intestine Large	intestine
36	chr9:110090600-110098000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr9:110090800-110097800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:110090800-110097800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr9:110091000-110097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:110091000-110103000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:110091200-110098200	Weak transcription	Psoas Muscle	Psoas
42	chr9:110091200-110099000	Weak transcription	Spleen	Spleen
43	chr9:110092000-110101800	Strong transcription	Primary T cells from cord blood	blood
44	chr9:110093000-110097800	Strong transcription	HSMMtube	muscle
45	chr9:110093000-110103400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr9:110093200-110101800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:110093200-110103200	Strong transcription	A549	lung
48	chr9:110093200-110103400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:110093400-110097800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr9:110094600-110101600	Strong transcription	H9 Cell Line	embryonic stem cell

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