Variant report

Variant	rs4952645
Chromosome Location	chr2:40949606-40949607
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1009356	0.82[CHB][hapmap];0.84[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs10197146	0.84[ASN][1000 genomes]
rs10445883	0.88[EUR][1000 genomes]
rs10490262	0.89[EUR][1000 genomes]
rs10490263	0.85[CEU][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs10490265	0.82[AFR][1000 genomes]
rs10490266	0.94[EUR][1000 genomes]
rs1107932	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11124757	0.89[EUR][1000 genomes]
rs11682329	0.84[EUR][1000 genomes]
rs11682367	0.83[EUR][1000 genomes]
rs11691011	0.94[EUR][1000 genomes]
rs11885458	0.83[EUR][1000 genomes]
rs11891229	0.83[EUR][1000 genomes]
rs12105490	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12463684	0.83[CEU][hapmap];0.82[CHB][hapmap];0.87[AFR][1000 genomes]
rs12466428	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12466466	0.83[AFR][1000 genomes]
rs12466571	0.80[EUR][1000 genomes]
rs12468195	0.84[ASN][1000 genomes]
rs12469295	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12712708	0.85[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs13016866	0.86[EUR][1000 genomes]
rs13414829	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13422403	0.83[ASN][1000 genomes]
rs17026547	0.84[ASN][1000 genomes]
rs1861305	0.89[EUR][1000 genomes]
rs1861306	0.90[EUR][1000 genomes]
rs2075195	0.89[EUR][1000 genomes]
rs2080341	0.89[EUR][1000 genomes]
rs2098360	0.89[EUR][1000 genomes]
rs2110786	0.82[EUR][1000 genomes]
rs2110791	0.87[AFR][1000 genomes]
rs2192816	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2192819	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2192820	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2216045	0.83[ASN][1000 genomes]
rs3851316	0.80[ASN][1000 genomes]
rs3862989	0.80[EUR][1000 genomes]
rs4101520	0.87[EUR][1000 genomes]
rs4528809	0.85[EUR][1000 genomes]
rs60819615	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62139540	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62139545	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62139546	0.80[ASN][1000 genomes]
rs62141367	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6544350	0.84[EUR][1000 genomes]
rs6712874	0.80[EUR][1000 genomes]
rs6714526	0.83[AFR][1000 genomes]
rs67918843	0.86[EUR][1000 genomes]
rs7562117	0.83[EUR][1000 genomes]
rs881189	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9808252	0.83[EUR][1000 genomes]
rs983123	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873931	chr2:40869165-40966719	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	nsv456441	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv581514	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv456452	chr2:40890416-40989061	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv581515	chr2:40890416-40989061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3584751	chr2:40916853-40952073	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
16	esv2754698	chr2:40922098-40949606	Flanking Active TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
17	esv34871	chr2:40922098-40951667	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
18	esv2755242	chr2:40922098-40951667	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
19	esv3584750	chr2:40926091-40949606	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
20	nsv1004050	chr2:40927363-40949606	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
21	esv3584749	chr2:40927375-40949606	Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
22	nsv961752	chr2:40929037-40950223	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
23	esv2756918	chr2:40930721-40966719	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
24	esv2759045	chr2:40930721-40966719	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4952645	TMEM178	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40947000-40951200	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:40947000-40952400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:40948600-40949800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:40949200-40961400	Weak transcription	HSMM	muscle
5	chr2:40949400-40952200	Weak transcription	HMEC	breast
6	chr2:40949400-40973200	Weak transcription	HSMMtube	muscle
7	chr2:40949600-40950200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:40949600-40950200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr2:40949600-40950200	Enhancers	Esophagus	oesophagus
10	chr2:40949600-40950200	Enhancers	Right Atrium	heart

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