Variant report

Variant	rs9409149
Chromosome Location	chr9:118162462-118162463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10124685	0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10817756	0.86[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817758	0.81[GIH][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10982719	0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10982722	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982724	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982726	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982743	0.83[EUR][1000 genomes]
rs10982755	0.82[EUR][1000 genomes]
rs10982757	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10982764	0.81[EUR][1000 genomes]
rs11791418	0.87[EUR][1000 genomes]
rs12336386	0.82[EUR][1000 genomes]
rs2067094	0.83[EUR][1000 genomes]
rs3750505	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018671	0.86[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7029620	0.84[EUR][1000 genomes]
rs7040283	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7040762	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7048279	0.80[EUR][1000 genomes]
rs7854183	0.80[EUR][1000 genomes]
rs7871775	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9408863	0.81[GIH][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9408864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9408865	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9408869	0.80[EUR][1000 genomes]
rs9409148	0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9409150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409155	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9409159	0.82[EUR][1000 genomes]
rs976734	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs981911	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1042957	chr9:118153824-118313540	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2761245	chr9:118157164-118171298	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	nsv519995	chr9:118157729-118163797	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9409149	DEC1	cis	cerebellum	SCAN
rs9409149	C9orf29	cis	parietal	SCAN
rs9409149	ZNF618	cis	parietal	SCAN
rs9409149	DNAJC25	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118158800-118162600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:118158800-118163200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:118159000-118170600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:118159200-118163000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:118159200-118163200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:118159200-118163200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:118159200-118163200	Weak transcription	NH-A	brain
8	chr9:118159200-118163800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:118160000-118164200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:118160400-118164600	Enhancers	NHDF-Ad	bronchial
11	chr9:118160400-118173600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:118160600-118163200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:118161400-118163000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:118161400-118163400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:118161600-118163200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr9:118161600-118163400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr9:118161800-118162600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr9:118161800-118162600	Weak transcription	Fetal Stomach	stomach
19	chr9:118161800-118163000	Weak transcription	Fetal Lung	lung
20	chr9:118162000-118163400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:118162200-118163000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:118162200-118163000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr9:118162200-118163000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:118162200-118166000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:118162200-118174000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:118162400-118165000	Enhancers	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links