Variant report

Variant	rs3003903
Chromosome Location	chr1:221949567-221949568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11118855	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11118856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11118863	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12034159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13375371	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3003902	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3010848	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3010852	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4403637	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7530733	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7551182	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 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	chr1:221945400-221949600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:221947400-221949600	Weak transcription	Hela-S3	cervix
3	chr1:221947600-221952000	Weak transcription	Spleen	Spleen
4	chr1:221947600-221953600	Weak transcription	Lung	lung
5	chr1:221948200-221950000	Weak transcription	Stomach Mucosa	stomach
6	chr1:221948200-221950000	Weak transcription	HUVEC	blood vessel
7	chr1:221948600-221950600	Flanking Active TSS	GM12878-XiMat	blood
8	chr1:221948600-221951000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr1:221948600-221951200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:221948800-221951400	Enhancers	Primary B cells from cord blood	blood
11	chr1:221948800-221955000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:221948800-221958200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:221949000-221953800	Weak transcription	Adipose Nuclei	Adipose
14	chr1:221949000-221954600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:221949000-221955000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:221949200-221953400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:221949400-221949800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:221949400-221958000	Enhancers	Primary monocytes fromperipheralblood	blood

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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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