Variant report

Variant	rs3820975
Chromosome Location	chr2:231118041-231118042
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231112287..231114146-chr2:231116342..231119362,3	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10164566	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10177685	0.92[ASN][1000 genomes]
rs10200874	0.92[ASN][1000 genomes]
rs10498245	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10498250	1.00[CHB][hapmap]
rs10933332	1.00[CHB][hapmap]
rs10933333	1.00[CHB][hapmap]
rs11900550	1.00[CHB][hapmap]
rs12472020	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12477360	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs13389060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs13395371	0.92[ASN][1000 genomes]
rs13422994	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1346311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16826911	0.84[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs16826917	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs16826921	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs16826952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16827171	1.00[CHB][hapmap]
rs16827179	1.00[CHB][hapmap]
rs1863674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863677	0.92[ASN][1000 genomes]
rs2081713	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2114588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2114590	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2162481	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2396741	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34839676	0.92[ASN][1000 genomes]
rs3769841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769842	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3769846	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs3813464	0.92[ASN][1000 genomes]
rs3829782	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41265097	0.84[AFR][1000 genomes]
rs4343458	0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4972943	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4972945	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4972948	1.00[CHB][hapmap]
rs4972951	1.00[CHB][hapmap]
rs4973302	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4973304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4973305	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4973306	0.84[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4973315	1.00[CHB][hapmap]
rs4973317	1.00[CHB][hapmap]
rs4973318	1.00[CHB][hapmap]
rs57003673	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57402789	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59020873	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59805999	0.85[EUR][1000 genomes]
rs61575136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62191186	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191188	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191189	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62191191	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191192	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191193	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191196	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191197	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191199	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191200	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191201	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62191202	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62192161	0.85[EUR][1000 genomes]
rs62193107	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62193138	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62193139	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62193140	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62193141	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62193142	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62193143	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62193147	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6756713	1.00[CHB][hapmap]
rs7576496	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591582	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9989792	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9989808	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231090200-231170000	Weak transcription	Spleen	Spleen
2	chr2:231092600-231118400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:231101800-231121600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr2:231103200-231118200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:231103800-231118200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:231107600-231119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:231109000-231118800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:231109600-231120800	Strong transcription	Primary B cells from cord blood	blood
9	chr2:231114200-231118200	Weak transcription	GM12878-XiMat	blood
10	chr2:231115000-231118800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:231116600-231120600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:231116800-231119200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:231117000-231118800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:231117000-231119400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:231117600-231119600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:231118000-231118800	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr2:231118000-231118800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:231118000-231119000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:231118000-231119200	Enhancers	Primary T cells from cord blood	blood
20	chr2:231118000-231119200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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