Variant report

Variant	rs2141823
Chromosome Location	chr7:3609712-3609713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:3598045..3599826-chr7:3607481..3609986,2	K562	blood:
2	chr7:3608810..3611760-chr7:3613102..3614702,2	MCF-7	breast:
3	chr7:3609002..3610756-chr7:3616407..3619133,2	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10224159	0.84[JPT][hapmap]
rs10227320	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10232765	0.95[JPT][hapmap]
rs10234480	0.91[ASN][1000 genomes]
rs10235815	0.90[JPT][hapmap]
rs10242223	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10246895	0.90[JPT][hapmap]
rs10252736	0.87[ASN][1000 genomes]
rs10255605	0.95[JPT][hapmap]
rs10262783	0.95[JPT][hapmap]
rs10270365	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10274465	0.85[JPT][hapmap]
rs10274899	0.81[ASN][1000 genomes]
rs10274978	0.85[JPT][hapmap]
rs10277545	0.95[JPT][hapmap]
rs10278205	0.95[JPT][hapmap]
rs10281401	0.90[JPT][hapmap]
rs10454314	0.95[JPT][hapmap]
rs10499335	0.81[CHB][hapmap]
rs10951245	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11761186	0.90[JPT][hapmap]
rs11764387	0.90[JPT][hapmap]
rs11765903	0.95[JPT][hapmap]
rs11767639	0.89[GIH][hapmap]
rs11771359	0.95[JPT][hapmap]
rs11975299	0.87[ASN][1000 genomes]
rs11977306	0.90[JPT][hapmap]
rs11981092	0.95[JPT][hapmap]
rs1202229	0.89[TSI][hapmap]
rs12667184	0.90[JPT][hapmap]
rs1357309	0.95[JPT][hapmap]
rs1357310	0.95[JPT][hapmap]
rs1357312	0.95[JPT][hapmap]
rs1403159	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1464534	0.90[JPT][hapmap]
rs1522501	0.83[JPT][hapmap]
rs1554497	0.90[JPT][hapmap]
rs1554498	0.90[JPT][hapmap]
rs1554502	0.95[JPT][hapmap]
rs1851419	0.80[JPT][hapmap]
rs1882431	0.95[JPT][hapmap]
rs1915981	0.95[JPT][hapmap]
rs1915982	0.95[JPT][hapmap]
rs1922012	0.87[ASN][1000 genomes]
rs1922018	0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs1972765	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs2090940	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2177167	0.90[JPT][hapmap]
rs2178625	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178627	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs2178628	0.86[ASW][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2204121	0.90[JPT][hapmap]
rs2222868	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2464614	0.92[LWK][hapmap];0.81[AFR][1000 genomes]
rs2614967	0.85[ASW][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap]
rs2614971	0.89[ASN][1000 genomes]
rs2686852	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2705600	0.94[ASN][1000 genomes]
rs2705608	0.95[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs2705613	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs28735285	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2879918	0.83[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4302734	0.95[JPT][hapmap]
rs4416738	0.90[ASN][1000 genomes]
rs4719943	0.85[JPT][hapmap]
rs4722735	0.90[JPT][hapmap]
rs4722830	0.95[JPT][hapmap]
rs4722850	0.90[JPT][hapmap]
rs6415253	0.90[JPT][hapmap]
rs6415254	0.95[JPT][hapmap]
rs6462068	0.85[JPT][hapmap]
rs6462069	0.90[JPT][hapmap]
rs6462071	0.84[JPT][hapmap]
rs6462166	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67199766	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6967281	0.95[JPT][hapmap]
rs6969082	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6969267	0.90[JPT][hapmap]
rs6969407	0.85[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7779688	0.90[JPT][hapmap]
rs7790430	0.95[JPT][hapmap]
rs7791343	0.90[JPT][hapmap]
rs7794534	0.90[JPT][hapmap]
rs7798141	0.90[JPT][hapmap]
rs7800089	0.85[JPT][hapmap]
rs7802106	0.95[JPT][hapmap]
rs7807065	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs7809446	0.90[JPT][hapmap]
rs7811384	0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs939912	0.95[JPT][hapmap]
rs939913	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs9791502	0.83[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs9791974	0.85[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.80[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9969296	0.81[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2764026	chr7:3365002-3618361	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1034716	chr7:3512406-3616155	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887334	chr7:3531275-3635105	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1023888	chr7:3539750-3638242	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1034298	chr7:3539750-3646251	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1029264	chr7:3549193-3622532	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv1840932	chr7:3585560-3618827	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv1792280	chr7:3592290-3668229	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv605907	chr7:3598581-3614784	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1022135	chr7:3601840-3618349	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1020806	chr7:3602348-3614788	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2757205	chr7:3602348-3630349	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv2759501	chr7:3602348-3630349	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1017012	chr7:3602397-3638242	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv538679	chr7:3602397-3638242	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv605908	chr7:3605340-3615334	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv605909	chr7:3605340-3638547	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv1028640	chr7:3606640-3617998	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1025521	chr7:3606640-3618349	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv1838607	chr7:3606640-3618361	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv2752641	chr7:3609495-3631115	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv1835418	chr7:3609712-3618143	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv517279	chr7:3609712-3618143	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv818474	chr7:3609712-3618143	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
31	esv2752926	chr7:3609712-3631115	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
32	esv2754251	chr7:3609712-3631115	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2141823	RNF216L	cis	parietal	SCAN
rs2141823	PRKAR1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3600600-3616600	Weak transcription	Gastric	stomach
2	chr7:3607200-3612400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:3608000-3612800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:3608800-3610400	Enhancers	HepG2	liver
5	chr7:3609000-3609800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr7:3609000-3610000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:3609000-3610200	Enhancers	Pancreas	Pancrea
8	chr7:3609200-3614000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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