Variant report

Variant	rs12815613
Chromosome Location	chr12:121407256-121407257
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	chr12:121401463..121403474-chr12:121406949..121408762,2	K562	blood:
2	chr12:121403725..121406245-chr12:121406756..121408586,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1105416	0.81[TSI][hapmap]
rs11065360	0.98[ASN][1000 genomes]
rs11065361	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168954	0.81[TSI][hapmap]
rs12821745	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12826999	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696363	0.84[TSI][hapmap]
rs1718211	0.81[TSI][hapmap]
rs2650006	0.81[TSI][hapmap]
rs28380723	0.98[ASN][1000 genomes]
rs3213547	0.89[CHB][hapmap]
rs3751149	0.89[CHB][hapmap]
rs3751151	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs3751152	0.89[CHB][hapmap]
rs55913575	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662739	0.81[TSI][hapmap]
rs66627474	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688402	0.81[TSI][hapmap]
rs694303	0.84[TSI][hapmap]
rs7135408	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73226265	0.98[ASN][1000 genomes]
rs7961554	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965349	0.83[MKK][hapmap]
rs9669493	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3357747	chr12:121405281-121427388	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Very long-chain saturated fatty acid levels (fatty acid 20:0)	25378659	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12815613	SPPL3	cis	cerebellum	SCAN
rs12815613	P2RX4	cis	cerebellum	SCAN
rs12815613	NOS1	cis	parietal	SCAN
rs12815613	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121394600-121408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:121395800-121408200	Weak transcription	Fetal Kidney	kidney
3	chr12:121400600-121416000	Weak transcription	Small Intestine	intestine
4	chr12:121403200-121409400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:121403800-121411000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:121404400-121408200	Weak transcription	Esophagus	oesophagus
7	chr12:121404600-121408000	Strong transcription	Fetal Intestine Small	intestine
8	chr12:121404800-121409000	Strong transcription	Fetal Intestine Large	intestine
9	chr12:121404800-121409800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr12:121405200-121415400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:121405400-121409000	Strong transcription	Pancreas	Pancrea
12	chr12:121405400-121409200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr12:121406400-121407400	Strong transcription	Fetal Stomach	stomach
14	chr12:121406600-121407400	Strong transcription	A549	lung
15	chr12:121406600-121408400	Strong transcription	Colonic Mucosa	Colon
16	chr12:121406600-121409000	Strong transcription	Gastric	stomach
17	chr12:121406600-121410800	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr12:121406600-121412400	Genic enhancers	Liver	Liver
19	chr12:121406800-121408400	Strong transcription	Stomach Mucosa	stomach
20	chr12:121407000-121407400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:121407000-121408200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:121407000-121409400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:121407200-121407800	Weak transcription	HepG2	liver
24	chr12:121407200-121409400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:121407200-121409800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links