Variant report

Variant	rs689979
Chromosome Location	chr9:98718673-98718674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10121403	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10481647	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739632	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10760675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10760692	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10818017	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10983692	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10983739	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs10983773	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10983818	0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs12004422	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12375861	0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs12553442	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2117432	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2164156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2164157	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs238	0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2770837	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3930253	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743458	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs583716	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs585223	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs601916	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs615866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617884	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs626264	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs631273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636456	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs640281	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs643815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479036	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];1.00[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];0.95[ASN][1000 genomes]
rs676453	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs678244	1.00[CEU][hapmap]
rs680468	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs680754	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];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs689627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs689820	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs690152	0.82[EUR][1000 genomes]
rs690222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs690304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690335	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs690420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690455	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs690484	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs700963	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7024710	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7028281	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868559	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7874897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs816676	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs816681	0.82[ASN][1000 genomes]
rs913408	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9409321	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9409322	0.93[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1035723	chr9:98701628-98734356	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs689979	C9orf130	cis	parietal	SCAN
rs689979	LINC00476	cis	Thyroid	GTEx
rs689979	LINC00476	cis	Stomach	GTEx
rs689979	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs689979	C9orf130	cis	cerebellum	SCAN
rs689979	LINC00476	cis	Nerve Tibial	GTEx
rs689979	LINC00476	cis	lung	GTEx
rs689979	PTPDC1	cis	parietal	SCAN
rs689979	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs689979	LINC00476	cis	Artery Aorta	GTEx
rs689979	LINC00476	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
2	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:98687800-98726000	Weak transcription	Gastric	stomach
4	chr9:98695800-98742400	Weak transcription	NHLF	lung
5	chr9:98705000-98718800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:98705400-98734200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
8	chr9:98706800-98734000	Weak transcription	Hela-S3	cervix
9	chr9:98709800-98718800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:98709800-98718800	Weak transcription	Right Ventricle	heart
11	chr9:98709800-98727800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:98710000-98719200	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:98710000-98720000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:98710000-98734200	Weak transcription	HMEC	breast
15	chr9:98710000-98735000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:98710400-98741400	Weak transcription	Brain Anterior Caudate	brain
17	chr9:98711000-98722000	Weak transcription	Brain Germinal Matrix	brain
18	chr9:98711000-98743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
20	chr9:98716200-98719400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:98716200-98719400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:98716200-98719400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:98716200-98719400	Strong transcription	Brain Cingulate Gyrus	brain
24	chr9:98716200-98719400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr9:98716200-98719400	Strong transcription	HSMM	muscle
26	chr9:98716200-98720000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:98716200-98720200	ZNF genes & repeats	Primary T cells from cord blood	blood
28	chr9:98716600-98719600	Strong transcription	Osteobl	bone
29	chr9:98716600-98720200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:98716600-98734400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr9:98716800-98719400	Strong transcription	Fetal Lung	lung
32	chr9:98716800-98720000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:98717000-98719400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:98717000-98719600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:98717000-98719800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
36	chr9:98717200-98719200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr9:98717200-98719200	Strong transcription	HSMMtube	muscle
38	chr9:98717200-98719600	Strong transcription	Fetal Thymus	thymus
39	chr9:98717800-98720200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:98718000-98720000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:98718000-98722600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:98718200-98719200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:98718200-98719200	ZNF genes & repeats	Brain Substantia Nigra	brain
44	chr9:98718200-98719400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:98718200-98719400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:98718200-98719400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr9:98718200-98719400	Strong transcription	Fetal Kidney	kidney
48	chr9:98718200-98719400	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:98718200-98719600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr9:98718200-98719800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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