Variant report

Variant	rs2296858
Chromosome Location	chr9:98803408-98803409
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98800086..98802107-chr9:98802951..98805065,2	K562	blood:
2	chr9:98800966..98802558-chr9:98803277..98805259,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10115110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10117340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10512242	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10512245	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10739705	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10760189	0.81[AMR][1000 genomes]
rs10760679	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10818899	0.87[AMR][1000 genomes]
rs10819650	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10819663	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10819668	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10819720	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10985156	0.80[AMR][1000 genomes]
rs10987963	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10988755	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10988817	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10989035	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1195130	0.94[AMR][1000 genomes]
rs11998982	0.81[AMR][1000 genomes]
rs12340954	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12345187	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12347675	0.90[AMR][1000 genomes]
rs12348051	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12349742	0.87[AMR][1000 genomes]
rs1327996	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1327997	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13298093	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13299166	0.81[AMR][1000 genomes]
rs1556026	0.93[EUR][1000 genomes]
rs2026031	0.87[AMR][1000 genomes]
rs2405372	0.85[AMR][1000 genomes]
rs2943532	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs589362	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs596413	0.94[AMR][1000 genomes]
rs603947	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs609296	0.85[AMR][1000 genomes]
rs617187	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs623438	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs624075	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs625105	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62559026	0.85[AMR][1000 genomes]
rs62559767	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs640297	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs649819	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs657451	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs666093	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs667705	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs671058	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs682682	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs684455	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs686048	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs689619	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689696	0.90[AMR][1000 genomes]
rs689697	0.90[AMR][1000 genomes]
rs689710	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs689738	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689761	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs689804	0.90[AMR][1000 genomes]
rs689860	0.81[AMR][1000 genomes]
rs689911	0.82[AMR][1000 genomes]
rs689986	0.90[AMR][1000 genomes]
rs690056	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690063	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690495	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690528	0.90[AMR][1000 genomes]
rs690633	0.90[AMR][1000 genomes]
rs694230	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7847393	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7847983	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs816682	0.82[AMR][1000 genomes]
rs816683	0.81[AMR][1000 genomes]
rs816684	0.81[AMR][1000 genomes]
rs966217	0.94[AMR][1000 genomes];0.82[EUR][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	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1809137	chr9:98798752-98823646	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2296858	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs2296858	ERCC6L2	cis	Artery Tibial	GTEx
rs2296858	C9orf102	cis	multi-tissue	Pritchard
rs2296858	ERCC6L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
2	chr9:98793600-98804600	Weak transcription	Fetal Heart	heart
3	chr9:98799200-98804600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:98801400-98809600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:98801600-98804200	Enhancers	Pancreas	Pancrea
6	chr9:98801600-98805400	Enhancers	Fetal Lung	lung
7	chr9:98801600-98809800	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:98801800-98805400	Enhancers	Fetal Stomach	stomach
9	chr9:98801800-98809800	Weak transcription	Brain Substantia Nigra	brain
10	chr9:98801800-98810200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:98802000-98803600	Enhancers	Gastric	stomach
12	chr9:98802000-98804800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:98802400-98803600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:98802400-98803600	Enhancers	Fetal Intestine Small	intestine
15	chr9:98802400-98803800	Bivalent Enhancer	Placenta	Placenta
16	chr9:98802400-98806200	Weak transcription	Spleen	Spleen
17	chr9:98802600-98803600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr9:98802600-98803600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr9:98802600-98803600	Enhancers	Fetal Intestine Large	intestine
20	chr9:98802600-98803600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr9:98802600-98803800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:98802600-98803800	Enhancers	Lung	lung
23	chr9:98802600-98804000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr9:98802800-98803600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:98802800-98803600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
26	chr9:98802800-98803600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:98802800-98803800	Enhancers	Fetal Muscle Trunk	muscle
28	chr9:98802800-98803800	Enhancers	Ovary	ovary
29	chr9:98802800-98803800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr9:98803000-98803600	Enhancers	Small Intestine	intestine
31	chr9:98803000-98803600	Flanking Active TSS	HepG2	liver
32	chr9:98803000-98804000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:98803000-98804400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:98803000-98804400	Bivalent Enhancer	Stomach Mucosa	stomach
35	chr9:98803000-98808600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:98803000-98810200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:98803200-98803600	Active TSS	A549	lung
38	chr9:98803200-98805200	Enhancers	Fetal Muscle Leg	muscle
39	chr9:98803400-98804000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:98803400-98807200	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links