Variant report

Variant	rs1541987
Chromosome Location	chr6:25950397-25950398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25948463..25951248-chr6:26020733..26023428,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196176	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10807007	0.86[JPT][hapmap]
rs10946800	1.00[CEU][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115920	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1130000	0.89[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs1165160	0.81[CHB][hapmap]
rs1165176	0.83[CHD][hapmap]
rs1165196	0.80[CHD][hapmap]
rs1165205	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs1165207	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs1165209	0.80[CHD][hapmap]
rs1165213	0.80[CHD][hapmap]
rs1165215	0.80[CHD][hapmap]
rs1184804	0.81[CHB][hapmap]
rs1185569	0.83[CHD][hapmap]
rs12195653	0.96[CEU][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12209482	0.81[EUR][1000 genomes]
rs1324084	0.82[EUR][1000 genomes]
rs1436306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436307	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1436308	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1436309	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1436310	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1540273	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1541988	0.89[ASN][1000 genomes]
rs1816546	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1865760	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2008015	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2013063	0.89[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs2032450	0.82[AMR][1000 genomes]
rs2051541	0.89[ASN][1000 genomes]
rs2051544	0.80[MEX][hapmap]
rs2071297	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2071298	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2071299	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2071300	0.89[GIH][hapmap]
rs2071301	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2157050	0.82[MEX][hapmap]
rs2164485	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328903	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2794719	0.80[MEX][hapmap]
rs2876693	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3752420	0.80[MEX][hapmap]
rs3752421	0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs3799371	0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs3799372	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3799373	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3830057	0.83[EUR][1000 genomes]
rs3846838	0.82[EUR][1000 genomes]
rs4478388	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56118523	0.82[EUR][1000 genomes]
rs566530	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs62394490	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6456705	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6910138	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6910174	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6915834	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6929805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932113	0.88[ASW][hapmap];0.87[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6938233	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6942196	0.80[MEX][hapmap]
rs7450342	0.93[GIH][hapmap]
rs7739966	0.82[EUR][1000 genomes]
rs7749342	0.93[GIH][hapmap]
rs7757666	0.82[EUR][1000 genomes]
rs7770139	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9295677	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9295679	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295680	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295687	0.80[MEX][hapmap]
rs9348698	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9348704	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9356991	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9358893	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9358895	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9358896	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9358903	0.86[JPT][hapmap]
rs9366634	0.80[MEX][hapmap]
rs9379802	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9379806	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9379807	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9379814	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9379815	0.83[ASN][1000 genomes]
rs9379818	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs9379819	0.86[JPT][hapmap]
rs9393675	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9393677	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393678	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393681	0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs9393683	0.90[CHD][hapmap];0.80[JPT][hapmap];0.80[MEX][hapmap]
rs942379	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs9461224	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9461227	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461230	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9467636	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9467641	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467645	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467646	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9467647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467648	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467650	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467651	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467656	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9467658	0.86[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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv5229	chr6:25912151-25956558	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1541987	HIST1H2BC	cis	cerebellum	SCAN
rs1541987	HIST1H2AA	cis	parietal	SCAN
rs1541987	HIST1H3D	cis	cerebellum	SCAN
rs1541987	HIST1H4B	cis	cerebellum	SCAN
rs1541987	HIST1H1C	cis	parietal	SCAN
rs1541987	HIST1H2BF	cis	parietal	SCAN
rs1541987	HIST1H3H	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25949400-25950400	Weak transcription	HepG2	liver

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