Variant report

Variant	rs640297
Chromosome Location	chr9:98764200-98764201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10115110	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10117340	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10125109	0.81[EUR][1000 genomes]
rs10512242	0.83[AMR][1000 genomes]
rs10512245	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739622	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10739705	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10760189	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10760261	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10760262	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10760269	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10760679	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10818574	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10818746	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10818899	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819650	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10819663	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10819668	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10819720	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10985156	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10985499	0.84[EUR][1000 genomes]
rs10985769	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10987963	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988755	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10988817	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10989035	0.86[AMR][1000 genomes]
rs1195130	0.90[AMR][1000 genomes]
rs11998982	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12000073	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12340954	0.87[AMR][1000 genomes]
rs12343734	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12345187	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12347675	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12348051	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12349742	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1327996	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1327997	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13289466	0.80[EUR][1000 genomes]
rs13294931	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13298093	0.83[AMR][1000 genomes]
rs13299166	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2026031	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2296858	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2405134	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2405371	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2405372	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2943532	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs589362	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs596413	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs603947	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs609296	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs617187	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623438	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624075	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625105	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62559026	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62559767	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6478977	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs649819	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657451	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666093	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667705	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs671058	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs682682	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs684455	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686048	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689619	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs689696	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs689697	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689710	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs689738	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs689744	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689761	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs689804	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs689860	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689911	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs689986	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690056	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690063	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690286	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs690495	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690528	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs690633	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs694230	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs700962	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7847393	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7847983	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871709	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs816670	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816672	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816673	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816674	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816675	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816678	0.82[EUR][1000 genomes]
rs816680	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs816683	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816684	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs966217	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs640297	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs640297	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs640297	ERCC6L2	cis	Artery Tibial	GTEx

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
4	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
6	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:98726400-98767800	Weak transcription	Gastric	stomach
9	chr9:98734600-98764400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:98734600-98782400	Weak transcription	NHEK	skin
12	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
13	chr9:98735800-98764200	Weak transcription	Placenta	Placenta
14	chr9:98735800-98766600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:98735800-98770600	Weak transcription	K562	blood
16	chr9:98735800-98771200	Weak transcription	HepG2	liver
17	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
18	chr9:98737000-98766800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr9:98741800-98778600	Weak transcription	NH-A	brain
20	chr9:98744600-98768000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:98744800-98766800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:98744800-98770800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr9:98744800-98771000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:98745000-98766800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:98747800-98782800	Weak transcription	Fetal Kidney	kidney
26	chr9:98748000-98764200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr9:98748000-98782600	Weak transcription	HMEC	breast
28	chr9:98748200-98771000	Weak transcription	Fetal Heart	heart
29	chr9:98748400-98764200	Weak transcription	Fetal Intestine Large	intestine
30	chr9:98748400-98766600	Weak transcription	HSMM	muscle
31	chr9:98748400-98767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:98748400-98767800	Weak transcription	NHLF	lung
33	chr9:98748400-98768400	Weak transcription	HSMMtube	muscle
34	chr9:98748400-98770600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:98748400-98782800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:98748600-98766800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:98748600-98781200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr9:98748800-98766600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:98748800-98766800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr9:98749400-98770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:98749600-98770200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr9:98750000-98766600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:98750200-98764400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr9:98750200-98764400	Weak transcription	Fetal Brain Female	brain
45	chr9:98750200-98766600	Weak transcription	Dnd41	blood
46	chr9:98750200-98766800	Weak transcription	Fetal Thymus	thymus
47	chr9:98750400-98764200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:98750400-98764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:98750400-98764200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:98750400-98768200	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links