Variant report

Variant	rs644080
Chromosome Location	chr21:40934470-40934471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12627708	1.00[JPT][hapmap]
rs1734930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2037669	0.82[ASN][1000 genomes]
rs2837074	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2989335	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs503729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506387	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs516865	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs523372	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526526	0.90[ASN][1000 genomes]
rs527343	0.90[ASN][1000 genomes]
rs528499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs529409	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs538333	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs542531	0.90[ASN][1000 genomes]
rs551439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs551624	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs551680	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs551830	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs554401	0.90[ASN][1000 genomes]
rs555963	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs561166	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs562285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs563230	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs563259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs564126	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs567837	0.90[ASN][1000 genomes]
rs568840	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579841	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs585092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs59155174	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs596320	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs602107	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs606003	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs606414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs611039	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs613758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs617259	0.90[ASN][1000 genomes]
rs626856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs629432	0.90[ASN][1000 genomes]
rs630270	0.90[ASN][1000 genomes]
rs631454	0.90[ASN][1000 genomes]
rs636599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs646823	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs650633	0.90[ASN][1000 genomes]
rs651607	0.90[ASN][1000 genomes]
rs657833	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658066	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs665778	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs689400	0.96[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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40928000-40935600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:40928600-40934800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr21:40928600-40936800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr21:40928600-40940200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr21:40928800-40935000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:40931600-40935800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr21:40931800-40940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:40932000-40935600	Enhancers	Stomach Mucosa	stomach
9	chr21:40932200-40935600	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr21:40932600-40936800	Enhancers	Duodenum Mucosa	Duodenum
11	chr21:40933000-40937000	Enhancers	Fetal Heart	heart
12	chr21:40933400-40935600	Enhancers	Right Ventricle	heart
13	chr21:40933400-40935800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr21:40933600-40934600	Weak transcription	Left Ventricle	heart
15	chr21:40933600-40934600	Weak transcription	Pancreas	Pancrea
16	chr21:40933600-40939000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr21:40934200-40937200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr21:40934200-40937400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr21:40934200-40937400	Enhancers	Brain Germinal Matrix	brain
20	chr21:40934400-40934600	Enhancers	Fetal Brain Male	brain
21	chr21:40934400-40934600	Enhancers	Right Atrium	heart
22	chr21:40934400-40934800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr21:40934400-40935800	Enhancers	Brain Anterior Caudate	brain
24	chr21:40934400-40936400	Enhancers	Fetal Brain Female	brain
25	chr21:40934400-40937200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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