Variant report

Variant	rs2839643
Chromosome Location	chr21:44602509-44602510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1041453	0.85[ASN][1000 genomes]
rs11203177	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11702241	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11909888	0.82[ASN][1000 genomes]
rs11910132	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839641	0.92[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839642	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839649	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28970980	0.82[ASN][1000 genomes]
rs28971677	0.82[ASN][1000 genomes]
rs4919966	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4919967	0.92[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7276342	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913812	chr21:44213057-44686358	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1067412	chr21:44526656-44772130	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1060276	chr21:44550394-44628579	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv913832	chr21:44579105-44768562	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44598400-44602800	Weak transcription	Brain Hippocampus Middle	brain
2	chr21:44599200-44603000	Weak transcription	Colonic Mucosa	Colon
3	chr21:44599200-44614200	Weak transcription	Right Atrium	heart
4	chr21:44600000-44605800	Weak transcription	Gastric	stomach
5	chr21:44600200-44611200	Weak transcription	Primary T cells from cord blood	blood
6	chr21:44600600-44603400	Enhancers	Fetal Brain Male	brain
7	chr21:44601200-44603000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr21:44601400-44603000	Flanking Active TSS	Fetal Brain Female	brain
9	chr21:44601600-44602600	Weak transcription	Fetal Muscle Leg	muscle
10	chr21:44601600-44604400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr21:44601600-44604600	Weak transcription	Esophagus	oesophagus
12	chr21:44601600-44605600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr21:44602000-44602600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr21:44602200-44603800	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr21:44602400-44602600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr21:44602400-44602600	Flanking Bivalent TSS/Enh	Spleen	Spleen
17	chr21:44602400-44602800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:44602400-44602800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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