Variant report

Variant	rs3789071
Chromosome Location	chr2:111802105-111802106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3789090	0.92[CEU][hapmap]
rs4849345	0.83[AMR][1000 genomes]
rs62163297	0.83[AMR][1000 genomes]
rs62163299	0.85[EUR][1000 genomes]
rs62163300	0.86[EUR][1000 genomes]
rs6717763	0.87[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs7563010	0.88[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs7602030	0.87[CEU][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap]
rs7603798	0.92[CEU][hapmap]
rs7604244	0.87[CEU][hapmap];0.81[TSI][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789071	MARCKSL1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:111797800-111806600	Weak transcription	Fetal Kidney	kidney
3	chr2:111799600-111804000	Enhancers	Fetal Thymus	thymus
4	chr2:111799600-111804400	Weak transcription	Pancreas	Pancrea
5	chr2:111800200-111803600	Enhancers	Primary T cells from cord blood	blood
6	chr2:111800400-111802200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:111800600-111802200	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr2:111800800-111802200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr2:111800800-111802200	Enhancers	GM12878-XiMat	blood
10	chr2:111801200-111807600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:111801600-111803000	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr2:111801600-111807400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:111801800-111802200	Bivalent Enhancer	Thymus	Thymus
14	chr2:111801800-111802600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:111801800-111806800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:111802000-111804600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:111802000-111807000	Weak transcription	Primary B cells from cord blood	blood

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Input of quick search could be:

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

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