Variant report

Variant	rs817836
Chromosome Location	chr9:110097621-110097622
allele	A/C
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: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10113916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10119641	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10122970	0.87[ASN][1000 genomes]
rs10481632	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10521083	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10732368	0.84[CHB][hapmap]
rs10739232	0.87[CHB][hapmap]
rs10739234	0.84[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10739236	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739238	0.84[CHB][hapmap];0.92[AFR][1000 genomes]
rs10759219	0.89[CHB][hapmap]
rs10759222	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs10759225	0.83[CHD][hapmap]
rs10816477	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10816480	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816485	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816490	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816498	1.00[YRI][hapmap]
rs10978767	0.94[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs10978769	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10978770	0.89[CHB][hapmap]
rs10978775	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978776	0.87[ASN][1000 genomes]
rs10978777	0.87[ASN][1000 genomes]
rs10978791	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342066	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12345455	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12551936	0.84[CEU][hapmap]
rs12555417	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1323808	0.84[CHB][hapmap]
rs1323809	0.83[CHD][hapmap]
rs1535765	0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1535766	0.89[CHB][hapmap]
rs1805329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805332	0.84[CHB][hapmap];0.91[CHD][hapmap]
rs1805334	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1805335	0.85[CHD][hapmap]
rs1886134	0.84[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1969798	0.80[AFR][1000 genomes]
rs1980725	0.80[AFR][1000 genomes]
rs2005143	0.82[ASN][1000 genomes]
rs2147071	0.85[AFR][1000 genomes]
rs2147072	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs2417776	0.87[ASN][1000 genomes]
rs2417784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417785	0.84[CHB][hapmap]
rs28534368	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28769087	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28848858	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4278207	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4481670	0.83[CHB][hapmap]
rs4625087	0.84[AFR][1000 genomes]
rs4978404	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4978406	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4978849	0.83[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs61701375	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs698475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025563	0.83[JPT][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7029997	0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7030169	0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7030555	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7030631	0.85[AFR][1000 genomes]
rs7031906	0.84[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs7035611	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7036284	0.87[ASN][1000 genomes]
rs7038737	0.83[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7039041	0.92[AFR][1000 genomes]
rs7040217	0.96[ASN][1000 genomes]
rs7041137	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7041497	0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7043962	0.86[AFR][1000 genomes]
rs7046950	0.84[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7852295	0.89[CHB][hapmap]
rs7856227	0.92[AFR][1000 genomes]
rs7866312	0.89[CHB][hapmap]
rs7866353	0.89[CHB][hapmap]
rs7866797	0.89[CHB][hapmap]
rs7867544	0.94[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs7873745	0.86[ASN][1000 genomes]
rs817838	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817839	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817840	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817841	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs817843	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817844	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817845	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817846	0.88[AFR][1000 genomes]
rs817847	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs817849	0.88[ASN][1000 genomes]
rs817851	0.88[ASN][1000 genomes]
rs942291	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs942292	0.88[CHD][hapmap]
rs942293	0.84[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9632893	0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9969728	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.87[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs817836	OR13C8	cis	cerebellum	SCAN
rs817836	TXN	cis	parietal	SCAN

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	chr9:110079800-110098000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:110080600-110097800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:110084000-110097800	Strong transcription	Hela-S3	cervix
10	chr9:110084800-110098800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:110085400-110097800	Strong transcription	Liver	Liver
12	chr9:110087200-110098600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr9:110087600-110103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:110088400-110097800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:110088400-110098800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:110088400-110101400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:110088600-110098200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:110088600-110098400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:110088600-110098600	Weak transcription	Fetal Brain Male	brain
21	chr9:110088600-110101600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:110089600-110097800	Strong transcription	Osteobl	bone
23	chr9:110089600-110098000	Strong transcription	K562	blood
24	chr9:110089800-110099400	Strong transcription	Placenta	Placenta
25	chr9:110090200-110097800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:110090400-110098600	Strong transcription	Fetal Muscle Leg	muscle
27	chr9:110090400-110098600	Strong transcription	HUVEC	blood vessel
28	chr9:110090400-110101800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:110090600-110097800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:110090600-110097800	Strong transcription	Fetal Intestine Large	intestine
31	chr9:110090600-110098000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr9:110090800-110097800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:110090800-110097800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr9:110091000-110103000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:110091200-110098200	Weak transcription	Psoas Muscle	Psoas
36	chr9:110091200-110099000	Weak transcription	Spleen	Spleen
37	chr9:110092000-110101800	Strong transcription	Primary T cells from cord blood	blood
38	chr9:110093000-110097800	Strong transcription	HSMMtube	muscle
39	chr9:110093000-110103400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr9:110093200-110101800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:110093200-110103200	Strong transcription	A549	lung
42	chr9:110093200-110103400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr9:110093400-110097800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr9:110094600-110101600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr9:110094800-110100800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:110094800-110101800	Strong transcription	Fetal Intestine Small	intestine
47	chr9:110095000-110104600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:110095400-110099600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:110095400-110101600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:110095600-110103400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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