Variant report

Variant	rs198941
Chromosome Location	chr5:53035301-53035302
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	chr5:52777916..52780456-chr5:53034020..53036335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134363	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10471875	0.84[ASN][1000 genomes]
rs1465445	0.94[CEU][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs1532163	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs1552649	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1559266	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs173905	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844696	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1844698	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs185603	1.00[YRI][hapmap]
rs187659	0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2130744	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs256083	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256087	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256090	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256095	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256097	0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs256100	0.83[ASN][1000 genomes]
rs256107	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs256108	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs256110	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256112	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs256113	0.94[ASN][1000 genomes]
rs256116	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256117	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2607501	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2607502	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2607509	0.85[ASN][1000 genomes]
rs2607511	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2636991	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2637027	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2637030	0.85[ASN][1000 genomes]
rs271213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs271214	0.85[ASN][1000 genomes]
rs271216	0.83[ASN][1000 genomes]
rs271217	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31302	0.85[ASN][1000 genomes]
rs31303	0.94[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs31304	1.00[YRI][hapmap]
rs31305	1.00[YRI][hapmap]
rs370594	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs372006	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs372135	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs375956	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs376566	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs381374	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs399141	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs403207	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4147740	0.83[CEU][hapmap];0.84[MEX][hapmap]
rs423014	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs423872	0.84[ASN][1000 genomes]
rs424955	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs429384	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs430427	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs431602	1.00[YRI][hapmap]
rs435187	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs439552	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs439641	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs449160	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530216	0.86[ASN][1000 genomes]
rs549131	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6881928	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs693995	0.84[ASN][1000 genomes]
rs7728496	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[ASN][1000 genomes]
rs7731940	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs786333	0.85[ASN][1000 genomes]
rs786335	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs813301	0.85[ASN][1000 genomes]
rs889291	0.89[JPT][hapmap]
rs889292	0.94[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs923609	0.88[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv881028	chr5:52965574-53035301	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv881185	chr5:52967967-53060893	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv830298	chr5:52973912-53193398	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv980643	chr5:53025294-53055999	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs198941	NDUFS4	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53034800-53035400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:53034800-53035400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:53034800-53035600	Enhancers	HMEC	breast
4	chr5:53035000-53035400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:53035000-53035400	Enhancers	Esophagus	oesophagus

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