Variant report

Variant	rs2989335
Chromosome Location	chr21:40927346-40927347
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	chr21:40919721..40922141-chr21:40925056..40927590,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1734930	0.90[ASN][1000 genomes]
rs2037669	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2837074	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837083	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492140	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs503729	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506387	0.90[ASN][1000 genomes]
rs516865	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs523372	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526526	0.90[ASN][1000 genomes]
rs527343	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs528499	0.90[ASN][1000 genomes]
rs529409	0.90[ASN][1000 genomes]
rs538333	0.90[ASN][1000 genomes]
rs542531	0.90[ASN][1000 genomes]
rs551439	0.90[ASN][1000 genomes]
rs551624	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs551680	0.90[ASN][1000 genomes]
rs551830	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs554401	0.90[ASN][1000 genomes]
rs555963	0.90[ASN][1000 genomes]
rs561166	0.90[ASN][1000 genomes]
rs562285	0.90[ASN][1000 genomes]
rs563230	0.90[ASN][1000 genomes]
rs563259	0.90[ASN][1000 genomes]
rs564126	0.90[ASN][1000 genomes]
rs567837	0.90[ASN][1000 genomes]
rs568840	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571227	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579841	1.00[ASN][1000 genomes]
rs585092	0.90[ASN][1000 genomes]
rs59155174	0.90[ASN][1000 genomes]
rs596320	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs602107	0.90[ASN][1000 genomes]
rs611039	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611958	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs613758	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs617259	0.90[ASN][1000 genomes]
rs626856	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628995	0.90[ASN][1000 genomes]
rs629432	0.90[ASN][1000 genomes]
rs630270	0.90[ASN][1000 genomes]
rs631454	0.90[ASN][1000 genomes]
rs636599	0.90[ASN][1000 genomes]
rs646823	0.90[ASN][1000 genomes]
rs650633	0.90[ASN][1000 genomes]
rs651607	0.90[ASN][1000 genomes]
rs657833	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658066	0.90[ASN][1000 genomes]
rs665778	0.90[ASN][1000 genomes]
rs689400	0.92[AFR][1000 genomes];0.98[EUR][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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	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
3	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv433457	chr21:40900348-40964553	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	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
8	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
9	esv17842	chr21:40918970-40965975	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40925600-40927800	Weak transcription	Brain Anterior Caudate	brain
2	chr21:40926600-40927800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr21:40926600-40927800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr21:40926600-40928000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr21:40926600-40928200	Weak transcription	Fetal Muscle Leg	muscle
6	chr21:40926800-40927800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40926800-40928000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr21:40926800-40928000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr21:40926800-40932600	Weak transcription	Right Ventricle	heart
10	chr21:40927000-40927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr21:40927000-40927400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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