Variant report

Variant	rs3789086
Chromosome Location	chr2:111794337-111794338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11123312	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11687123	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13012948	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13025923	0.86[ASN][1000 genomes]
rs17041761	0.89[JPT][hapmap]
rs1976055	0.86[ASN][1000 genomes]
rs35761487	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35816855	0.86[ASN][1000 genomes]
rs3789076	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3789087	0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3789088	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3827541	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56068469	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs59554295	0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111786000-111795800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:111787400-111795600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:111788200-111799200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:111790800-111799200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:111790800-111800200	Weak transcription	Spleen	Spleen
7	chr2:111791200-111794600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:111791200-111795600	Weak transcription	Gastric	stomach
9	chr2:111791200-111795800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:111792400-111796600	Weak transcription	Fetal Lung	lung
11	chr2:111792400-111797200	Weak transcription	Fetal Heart	heart
12	chr2:111792800-111797200	Weak transcription	Fetal Intestine Small	intestine
13	chr2:111792800-111801600	Weak transcription	Fetal Intestine Large	intestine
14	chr2:111793000-111796600	Weak transcription	Fetal Kidney	kidney
15	chr2:111793400-111796000	Enhancers	Primary B cells from cord blood	blood
16	chr2:111793400-111796000	Enhancers	Fetal Thymus	thymus
17	chr2:111793600-111795400	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:111793600-111795400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:111794000-111795200	Enhancers	GM12878-XiMat	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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