Variant report

Variant	rs10180123
Chromosome Location	chr2:52694032-52694033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10168435	0.93[ASN][1000 genomes]
rs10175067	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10176058	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10176819	0.93[ASN][1000 genomes]
rs10178979	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10186709	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10189311	0.93[ASN][1000 genomes]
rs10191908	0.93[ASN][1000 genomes]
rs10192786	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10196303	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10208214	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11125427	0.98[ASN][1000 genomes]
rs11125428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11891667	0.84[CHB][hapmap]
rs12052444	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12611666	0.98[ASN][1000 genomes]
rs12614961	0.98[ASN][1000 genomes]
rs12617648	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12713202	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713203	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713204	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13020964	0.85[CHB][hapmap]
rs13390149	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344587	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2081373	0.83[EUR][1000 genomes]
rs2098807	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2694133	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2727872	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4588226	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971823	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971829	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6545276	0.85[CHB][hapmap]
rs6708016	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6718567	0.84[ASN][1000 genomes]
rs6759941	0.89[AMR][1000 genomes]
rs7560361	0.98[ASN][1000 genomes]
rs7599425	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1007633	chr2:52217555-52862389	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv535714	chr2:52217555-52862389	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874111	chr2:52383698-52962055	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1014619	chr2:52496317-52821980	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv535717	chr2:52496317-52821980	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv998227	chr2:52527889-52821980	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv581929	chr2:52599360-52761239	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv874117	chr2:52633563-52745557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv874119	chr2:52646336-52694638	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv874120	chr2:52659874-52745557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv874121	chr2:52667944-52724060	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv874122	chr2:52667944-52730021	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1007170	chr2:52681191-52703416	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv2760562	chr2:52681203-52781542	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	esv1831158	chr2:52692840-52785972	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52684400-52694400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:52691000-52698000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:52692400-52694200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:52694000-52694200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:52694000-52694200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:52694000-52694800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:52694000-52694800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:52694000-52694800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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