Variant report

Variant	rs10759637
Chromosome Location	chr9:116025024-116025025
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116023106..116028620-chr9:116032404..116039334,10	MCF-7	breast:
2	chr9:116024571..116026114-chr9:116029017..116030804,2	K562	blood:
3	chr9:116024711..116027399-chr9:116031082..116034074,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10123415	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10125992	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513189	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739388	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739390	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739392	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10759633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10759636	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759638	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10817461	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10817468	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10981715	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs11789755	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs11792628	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12343629	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2296073	0.82[CHB][hapmap]
rs3750532	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs3750533	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs3750534	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs4129395	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129396	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4129397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4284098	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560868	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4979226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4979231	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6477998	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477999	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7038769	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7041615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7851395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859354	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9299214	0.81[CHB][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10759637	CDC26	cis	Esophagus Muscularis	GTEx
rs10759637	CDC26	cis	Adipose Subcutaneous	GTEx
rs10759637	CDC26	cis	Muscle Skeletal	GTEx
rs10759637	ZNF618	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:116009600-116029800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
5	chr9:116011400-116028800	Weak transcription	Fetal Kidney	kidney
6	chr9:116017400-116025800	Strong transcription	Fetal Muscle Leg	muscle
7	chr9:116017600-116026400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:116017600-116031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:116017800-116025200	Strong transcription	Left Ventricle	heart
10	chr9:116017800-116025400	Strong transcription	Fetal Brain Female	brain
11	chr9:116017800-116026400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:116018000-116027600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:116018200-116026200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:116018400-116025200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:116018400-116026000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:116018600-116026000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr9:116019000-116025200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:116019000-116026000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr9:116019200-116025200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr9:116019200-116025200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:116019200-116025400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:116019200-116028800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr9:116019400-116025200	Strong transcription	Adipose Nuclei	Adipose
25	chr9:116019400-116025400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:116019400-116025800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:116019800-116025400	Strong transcription	Placenta	Placenta
29	chr9:116020000-116025200	Strong transcription	HSMM	muscle
30	chr9:116020000-116029600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:116020200-116026000	Strong transcription	Brain Anterior Caudate	brain
32	chr9:116020600-116025600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:116020600-116027400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:116020600-116031600	Weak transcription	HUVEC	blood vessel
35	chr9:116020800-116025600	Strong transcription	Brain Germinal Matrix	brain
36	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
37	chr9:116021200-116031600	Weak transcription	Fetal Brain Male	brain
38	chr9:116021200-116032200	Weak transcription	Small Intestine	intestine
39	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:116021400-116025600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr9:116021400-116029800	Weak transcription	Primary B cells from cord blood	blood
42	chr9:116021400-116032200	Weak transcription	Pancreas	Pancrea
43	chr9:116021800-116025400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:116022200-116025200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr9:116022200-116025400	Strong transcription	Brain Angular Gyrus	brain
46	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
47	chr9:116022600-116028600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:116022600-116029400	Weak transcription	NH-A	brain
49	chr9:116022600-116031600	Weak transcription	NHDF-Ad	bronchial
50	chr9:116022800-116027200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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