Variant report

Variant	rs12684445
Chromosome Location	chr9:98805260-98805261
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10988804	0.82[GIH][hapmap];0.80[JPT][hapmap];0.82[MEX][hapmap]
rs11788050	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360064	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs16910298	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs16910418	0.80[JPT][hapmap]
rs1999023	0.82[GIH][hapmap];0.80[JPT][hapmap];0.81[MEX][hapmap]
rs2069053	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs3780574	0.80[JPT][hapmap]
rs4742775	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs4742781	0.80[JPT][hapmap];0.82[MEX][hapmap]
rs4743372	0.85[JPT][hapmap]
rs4743436	0.80[JPT][hapmap]
rs4743472	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4743479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868270	0.80[JPT][hapmap]

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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12684445	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs12684445	CAST	trans	parietal	SCAN
rs12684445	LINC00476	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
2	chr9:98801400-98809600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:98801600-98805400	Enhancers	Fetal Lung	lung
4	chr9:98801600-98809800	Weak transcription	Brain Hippocampus Middle	brain
5	chr9:98801800-98805400	Enhancers	Fetal Stomach	stomach
6	chr9:98801800-98809800	Weak transcription	Brain Substantia Nigra	brain
7	chr9:98801800-98810200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:98802400-98806200	Weak transcription	Spleen	Spleen
9	chr9:98803000-98808600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:98803000-98810200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:98803400-98807200	Enhancers	HSMMtube	muscle
12	chr9:98803600-98809000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:98803600-98809000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:98803800-98810200	Weak transcription	Ovary	ovary
15	chr9:98804600-98810200	Weak transcription	Fetal Intestine Small	intestine
16	chr9:98805000-98806000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:98805200-98807800	Weak transcription	Gastric	stomach
18	chr9:98805200-98809600	Weak transcription	Pancreas	Pancrea

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links