Variant report

Variant	rs3794775
Chromosome Location	chr17:16832370-16832371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11653942	0.87[JPT][hapmap]
rs11871817	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12937994	0.83[AFR][1000 genomes]
rs3751987	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs3751988	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs3751995	0.81[EUR][1000 genomes]
rs3751996	0.83[AFR][1000 genomes]
rs3751997	0.83[AFR][1000 genomes]
rs3752005	0.84[CEU][hapmap]
rs3752007	0.83[AFR][1000 genomes]
rs3752009	0.87[JPT][hapmap]
rs3764409	0.82[AFR][1000 genomes]
rs3794774	0.91[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3829585	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4792794	0.83[AFR][1000 genomes]
rs4792796	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55898532	0.81[EUR][1000 genomes]
rs6502537	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2753951	chr17:16660721-16848750	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2755100	chr17:16660721-16848750	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv526289	chr17:16821625-16837365	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3794775	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16827600-16832400	Weak transcription	Spleen	Spleen
2	chr17:16831200-16832800	Enhancers	Primary T cells from cord blood	blood
3	chr17:16831400-16834800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:16831600-16832800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:16831600-16834000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr17:16831800-16832400	Enhancers	Fetal Thymus	thymus
7	chr17:16831800-16832600	Enhancers	Left Ventricle	heart
8	chr17:16831800-16832800	Enhancers	Fetal Heart	heart
9	chr17:16832000-16832400	Enhancers	Adipose Nuclei	Adipose
10	chr17:16832000-16832600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr17:16832000-16832800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr17:16832000-16832800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr17:16832000-16832800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr17:16832000-16832800	Enhancers	Placenta	Placenta
15	chr17:16832200-16832400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:16832200-16832400	Enhancers	Brain Anterior Caudate	brain
17	chr17:16832200-16832600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr17:16832200-16835800	Weak transcription	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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