Variant report

Variant	rs11780500
Chromosome Location	chr8:99758904-99758905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10447977	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10755896	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs10755897	0.82[CHB][hapmap];0.83[CHD][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs10955186	0.90[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs10955187	0.90[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs10955189	0.81[AMR][1000 genomes]
rs10955190	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11774463	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11778767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11785245	0.90[JPT][hapmap]
rs12114834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12541317	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12542758	1.00[YRI][hapmap]
rs12547297	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs12549803	0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs12550783	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs12677183	0.86[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs12679734	0.91[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12680195	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs13269932	0.86[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes]
rs13275915	0.86[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13279438	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1447245	0.86[CHB][hapmap]
rs1476181	0.95[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1961744	0.81[AMR][1000 genomes]
rs2442012	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2442014	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2515214	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2515216	1.00[GIH][hapmap];0.95[TSI][hapmap]
rs2922066	0.86[CHB][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2922073	0.81[AMR][1000 genomes]
rs2922074	0.81[AMR][1000 genomes]
rs2922075	0.85[AMR][1000 genomes]
rs2922076	0.91[CHB][hapmap];0.81[AMR][1000 genomes]
rs2922078	0.95[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs2922081	0.85[AMR][1000 genomes]
rs2922082	0.91[CHB][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs3019293	0.85[AMR][1000 genomes]
rs34114299	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs34281206	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34366206	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34855977	0.87[AMR][1000 genomes]
rs35536167	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35798019	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35804297	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35915594	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4131873	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4255105	0.91[CHB][hapmap];0.87[CHD][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4279561	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4292660	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs4304299	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4323440	0.84[ASN][1000 genomes]
rs4413739	0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4440607	0.86[AMR][1000 genomes]
rs4509292	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4517094	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4541872	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4549741	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4562286	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4612309	0.85[AMR][1000 genomes]
rs4734410	0.86[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs4734414	0.82[AMR][1000 genomes]
rs4735568	0.85[TSI][hapmap]
rs4735569	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4735574	0.84[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs57034072	0.84[ASN][1000 genomes]
rs58321500	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62532565	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62532577	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62532587	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6651182	0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs6988087	0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6992925	0.86[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs72666694	0.86[ASN][1000 genomes]
rs7818828	0.86[JPT][hapmap];0.85[TSI][hapmap]
rs7838239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7845271	0.93[GIH][hapmap];0.81[TSI][hapmap]
rs9656842	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11780500	NCALD	cis	cerebellum	SCAN
rs11780500	OSR2	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99739600-99776400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:99741600-99794200	Weak transcription	Pancreas	Pancrea
3	chr8:99743200-99763400	Weak transcription	Right Ventricle	heart
4	chr8:99743400-99777200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:99746600-99789400	Weak transcription	Psoas Muscle	Psoas
6	chr8:99747800-99763000	Weak transcription	Osteobl	bone
7	chr8:99748000-99759000	Weak transcription	NHDF-Ad	bronchial
8	chr8:99748600-99777200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:99751000-99760800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:99754200-99761600	Weak transcription	HSMMtube	muscle
11	chr8:99754200-99777600	Weak transcription	Left Ventricle	heart
12	chr8:99756200-99776800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:99756600-99777200	Weak transcription	HMEC	breast
14	chr8:99756800-99760600	Weak transcription	Brain Hippocampus Middle	brain
15	chr8:99756800-99776400	Weak transcription	Placenta	Placenta
16	chr8:99757000-99759200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr8:99757000-99760000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:99757000-99760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr8:99757000-99761600	Weak transcription	HUVEC	blood vessel
20	chr8:99757200-99759200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr8:99757200-99759200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr8:99757200-99759200	Strong transcription	Liver	Liver
23	chr8:99757200-99759400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr8:99757200-99759400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:99757200-99760200	ZNF genes & repeats	Dnd41	blood
26	chr8:99757400-99759200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr8:99757400-99759400	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr8:99757400-99763200	Weak transcription	K562	blood
29	chr8:99757400-99777600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr8:99757400-99777800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr8:99757400-99777800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr8:99757400-99778600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr8:99757600-99762800	Weak transcription	Colon Smooth Muscle	Colon
34	chr8:99757800-99759200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr8:99757800-99760200	ZNF genes & repeats	GM12878-XiMat	blood
36	chr8:99758000-99759200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:99758000-99759200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:99758000-99759200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr8:99758000-99759200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr8:99758000-99759200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr8:99758000-99759200	ZNF genes & repeats	Fetal Heart	heart
42	chr8:99758000-99763600	Weak transcription	Small Intestine	intestine
43	chr8:99758200-99759400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:99758400-99759200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr8:99758400-99759200	Weak transcription	Fetal Kidney	kidney
46	chr8:99758400-99759800	Weak transcription	Primary B cells from cord blood	blood
47	chr8:99758400-99760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr8:99758400-99763400	Weak transcription	NH-A	brain
49	chr8:99758400-99768800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr8:99758400-99772800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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