Variant report

Variant	rs16961883
Chromosome Location	chr17:45099425-45099426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11649831	0.80[ASN][1000 genomes]
rs11654437	0.93[ASN][1000 genomes]
rs11656799	0.85[ASN][1000 genomes]
rs11657519	0.85[ASN][1000 genomes]
rs11657664	0.93[ASN][1000 genomes]
rs11657803	0.85[ASN][1000 genomes]
rs16941444	0.85[ASN][1000 genomes]
rs17676673	1.00[CEU][hapmap]
rs2678713	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs28376067	0.93[ASN][1000 genomes]
rs2907245	0.94[ASN][1000 genomes]
rs2959964	0.93[ASN][1000 genomes]
rs35936425	0.80[ASN][1000 genomes]
rs3851791	0.86[GIH][hapmap]
rs55858176	0.81[EUR][1000 genomes]
rs56200895	0.80[ASN][1000 genomes]
rs57418075	0.80[ASN][1000 genomes]
rs7214920	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap]
rs8067246	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong 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 target site	21 gene(s)	inside rSNPs	diseases
9	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
10	esv1849526	chr17:45087601-45132750	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv9565	chr17:45088304-45135259	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv962331	chr17:45088443-45141744	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	esv1843358	chr17:45090768-45141959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
14	esv16081	chr17:45091145-45133206	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
15	esv1851648	chr17:45091619-45146146	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
16	esv1846431	chr17:45092987-45145946	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
17	esv1843137	chr17:45099247-45132750	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16961883	GOSR2	cis	multi-tissue	Pritchard
rs16961883	MYL4	cis	multi-tissue	Pritchard
rs16961883	IGFBP4	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45057200-45100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:45062200-45113200	Weak transcription	Ovary	ovary
3	chr17:45075200-45130200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr17:45083400-45107000	Weak transcription	Lung	lung
5	chr17:45086000-45129600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:45086000-45129600	Weak transcription	Fetal Muscle Leg	muscle
7	chr17:45086800-45129600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr17:45087200-45111400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:45087200-45126600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr17:45087600-45129600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr17:45088600-45128600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:45090000-45131600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr17:45090200-45131000	Weak transcription	Dnd41	blood
14	chr17:45090600-45100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr17:45090600-45103600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:45090600-45129600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr17:45091200-45129600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr17:45093400-45111200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr17:45094200-45129600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:45094400-45105200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr17:45095000-45130200	Weak transcription	Brain Anterior Caudate	brain
22	chr17:45095200-45101800	Weak transcription	Adipose Nuclei	Adipose
23	chr17:45095200-45109600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:45096000-45103400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr17:45096200-45131000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:45096400-45112000	Weak transcription	Fetal Intestine Small	intestine
27	chr17:45096400-45129600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:45096800-45129600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:45096800-45129600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr17:45097000-45105200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:45097400-45109200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:45097400-45129600	Weak transcription	Fetal Stomach	stomach

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