Variant report

Variant	rs11962550
Chromosome Location	chr6:2350630-2350631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11242758	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11963138	0.82[ASN][1000 genomes]
rs12191002	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13196306	0.81[ASN][1000 genomes]
rs13217030	0.82[ASN][1000 genomes]
rs2295008	0.80[ASN][1000 genomes]
rs2450299	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450304	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2450307	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2450310	0.85[EUR][1000 genomes]
rs2479001	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479002	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479004	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2479008	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2479011	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2479014	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505657	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505658	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505659	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505660	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505661	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505662	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2505663	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505666	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505667	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505670	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505671	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505673	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505677	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505678	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3823287	0.82[ASN][1000 genomes]
rs6596879	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7754950	0.82[ASN][1000 genomes]
rs9328087	0.82[ASN][1000 genomes]
rs9378688	0.82[ASN][1000 genomes]
rs9378692	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378693	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9391946	0.82[ASN][1000 genomes]
rs9392375	0.82[ASN][1000 genomes]
rs9392377	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
5	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
7	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11962550	LOC728772///TMEM106A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2339200-2370000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:2344400-2353600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:2344400-2377400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:2345400-2365800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:2345600-2353800	Weak transcription	Fetal Stomach	stomach
6	chr6:2346600-2352000	Weak transcription	Aorta	Aorta
7	chr6:2346600-2353800	Weak transcription	HepG2	liver
8	chr6:2347000-2351000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:2347000-2362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:2347400-2352000	Weak transcription	HSMMtube	muscle
11	chr6:2349400-2362000	Weak transcription	Spleen	Spleen
12	chr6:2349600-2353800	Weak transcription	Stomach Mucosa	stomach
13	chr6:2350000-2356600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:2350600-2353800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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