Variant report

Variant	rs399324
Chromosome Location	chr21:41114980-41114981
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr21:41114532-41115040	MCF-7	breast:	n/a	chr21:41114819-41114833
2	GATA3	chr21:41114571-41115025	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:41085205..41088011-chr21:41112686..41115638,2	MCF-7	breast:

Variant related genes	Relation type
IGSF5	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10470189	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1077589	0.92[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1077590	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1077591	0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1235466	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1235467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1235468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1235475	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1235476	0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1235478	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12482872	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12483010	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1571711	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1614870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1624691	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1734853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1734854	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1734857	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1734858	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1734859	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1735142	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1735143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1735145	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1735146	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1735147	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1735149	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1735151	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2253741	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253748	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2253751	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2253752	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2266513	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2410179	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2410180	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2410181	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2837149	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837150	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837151	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837153	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837154	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837155	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837157	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837158	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837159	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837160	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837161	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837162	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837163	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837164	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837165	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837166	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2837168	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837169	0.86[CEU][hapmap];0.85[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837170	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837171	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837172	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837173	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837184	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898385	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2974990	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2989331	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs372997	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs386856	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs388152	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs388332	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs396774	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs399638	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs403249	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403527	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs412661	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs413515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs415340	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs415794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418566	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs421549	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs424447	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs425320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs431359	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs431735	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs431767	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs432185	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443468	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs460528	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4816645	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4816646	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4816648	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4816649	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4816650	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs4816651	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4816654	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4816655	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818083	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818085	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4818086	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4995787	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517561	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517562	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517565	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71316138	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7275687	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7278720	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7278858	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282199	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282336	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282400	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282429	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7282589	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7282623	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs741867	0.92[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs744568	0.92[CEU][hapmap];0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9305678	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9753841	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9753866	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9980150	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1065086	chr21:41034806-41429078	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv544445	chr21:41034806-41429078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv834099	chr21:41076873-41206030	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv275236	chr21:41110282-41119411	Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41104200-41138400	Weak transcription	Pancreas	Pancrea
2	chr21:41107800-41119400	Enhancers	Placenta	Placenta
3	chr21:41110000-41148400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr21:41113800-41115600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:41113800-41116000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr21:41114600-41117000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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