Variant report

Variant	rs2839642
Chromosome Location	chr21:44602306-44602307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1041453	0.85[ASN][1000 genomes]
rs11203177	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs11702241	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11909888	0.82[ASN][1000 genomes]
rs11910132	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839641	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2839643	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	0.86[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];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2839642	TMPRSS3	cis	cerebellum	SCAN
rs2839642	KRTAP12-4	cis	parietal	SCAN
rs2839642	PDE9A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44595600-44602400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr21:44596800-44602400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr21:44598400-44602800	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:44599200-44603000	Weak transcription	Colonic Mucosa	Colon
5	chr21:44599200-44614200	Weak transcription	Right Atrium	heart
6	chr21:44600000-44605800	Weak transcription	Gastric	stomach
7	chr21:44600200-44611200	Weak transcription	Primary T cells from cord blood	blood
8	chr21:44600600-44603400	Enhancers	Fetal Brain Male	brain
9	chr21:44601200-44603000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr21:44601400-44603000	Flanking Active TSS	Fetal Brain Female	brain
11	chr21:44601600-44602400	Enhancers	Brain Cingulate Gyrus	brain
12	chr21:44601600-44602600	Weak transcription	Fetal Muscle Leg	muscle
13	chr21:44601600-44604400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr21:44601600-44604600	Weak transcription	Esophagus	oesophagus
15	chr21:44601600-44605600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr21:44602000-44602600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:44602200-44602400	Weak transcription	Spleen	Spleen
18	chr21:44602200-44603800	Flanking Active TSS	Brain Germinal Matrix	brain

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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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