Variant report

Variant	rs16940337
Chromosome Location	chr18:13302390-13302391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13293376..13296291-chr18:13300592..13303207,3	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1551364	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1573507	0.84[GIH][hapmap];1.00[ASN][1000 genomes]
rs56359994	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56398323	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6505796	0.93[ASW][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67133687	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8084152	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv2209	chr18:13276410-13316570	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16940337	SLMO1	cis	parietal	SCAN
rs16940337	CIDEA	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13274600-13302400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:13285000-13316200	Weak transcription	Aorta	Aorta
3	chr18:13285400-13302600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr18:13295600-13312600	Weak transcription	Dnd41	blood
5	chr18:13297600-13302400	Weak transcription	Primary T cells from cord blood	blood
6	chr18:13298600-13303000	Weak transcription	Gastric	stomach
7	chr18:13298800-13302600	Enhancers	Fetal Brain Male	brain
8	chr18:13298800-13303400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:13298800-13314600	Weak transcription	Fetal Intestine Small	intestine
10	chr18:13299800-13303200	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr18:13299800-13303400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr18:13299800-13304200	Enhancers	Fetal Muscle Leg	muscle
13	chr18:13299800-13304600	Enhancers	Left Ventricle	heart
14	chr18:13300000-13303200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr18:13300000-13303400	Enhancers	Right Ventricle	heart
16	chr18:13300400-13304400	Weak transcription	Pancreas	Pancrea
17	chr18:13300600-13302600	Weak transcription	Lung	lung
18	chr18:13301200-13302400	Weak transcription	Spleen	Spleen
19	chr18:13301200-13304400	Enhancers	Fetal Thymus	thymus
20	chr18:13301200-13308400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr18:13301400-13303200	Enhancers	Brain Angular Gyrus	brain
22	chr18:13301400-13303600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:13301400-13304000	Enhancers	Brain Germinal Matrix	brain
24	chr18:13301600-13302400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr18:13301600-13302600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr18:13301600-13302600	Enhancers	Fetal Kidney	kidney
27	chr18:13301600-13302800	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr18:13301600-13303000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:13301600-13303400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr18:13301600-13304000	Enhancers	Brain Substantia Nigra	brain
31	chr18:13301600-13304200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr18:13301600-13304200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr18:13301600-13304600	Enhancers	Brain Hippocampus Middle	brain
34	chr18:13301800-13302400	Enhancers	Stomach Smooth Muscle	stomach
35	chr18:13301800-13302600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr18:13301800-13303000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr18:13301800-13303000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:13301800-13303200	Enhancers	Rectal Smooth Muscle	rectum
39	chr18:13301800-13303400	Enhancers	Fetal Lung	lung
40	chr18:13301800-13303400	Enhancers	Fetal Stomach	stomach
41	chr18:13301800-13303600	Enhancers	Colon Smooth Muscle	Colon
42	chr18:13301800-13304000	Enhancers	Thymus	Thymus
43	chr18:13301800-13304200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr18:13301800-13304600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr18:13301800-13305800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:13302000-13302400	Weak transcription	HSMMtube	muscle
47	chr18:13302000-13302800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr18:13302000-13302800	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr18:13302000-13303000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr18:13302000-13303000	Enhancers	HUES6 Cell Line	embryonic stem cell

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