Variant report

Variant	rs9960998
Chromosome Location	chr18:13302602-13302603
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:
2	chr18:13286615..13289389-chr18:13302517..13304559,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11659839	0.89[ASN][1000 genomes]
rs11659895	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11663785	1.00[JPT][hapmap]
rs12458323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs60418393	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62097350	0.85[ASN][1000 genomes]

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
rs9960998	CIDEA	cis	parietal	SCAN
rs9960998	C18orf19	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13285000-13316200	Weak transcription	Aorta	Aorta
2	chr18:13295600-13312600	Weak transcription	Dnd41	blood
3	chr18:13298600-13303000	Weak transcription	Gastric	stomach
4	chr18:13298800-13303400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:13298800-13314600	Weak transcription	Fetal Intestine Small	intestine
6	chr18:13299800-13303200	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr18:13299800-13303400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr18:13299800-13304200	Enhancers	Fetal Muscle Leg	muscle
9	chr18:13299800-13304600	Enhancers	Left Ventricle	heart
10	chr18:13300000-13303200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr18:13300000-13303400	Enhancers	Right Ventricle	heart
12	chr18:13300400-13304400	Weak transcription	Pancreas	Pancrea
13	chr18:13301200-13304400	Enhancers	Fetal Thymus	thymus
14	chr18:13301200-13308400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr18:13301400-13303200	Enhancers	Brain Angular Gyrus	brain
16	chr18:13301400-13303600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr18:13301400-13304000	Enhancers	Brain Germinal Matrix	brain
18	chr18:13301600-13302800	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr18:13301600-13303000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr18:13301600-13303400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr18:13301600-13304000	Enhancers	Brain Substantia Nigra	brain
22	chr18:13301600-13304200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr18:13301600-13304200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr18:13301600-13304600	Enhancers	Brain Hippocampus Middle	brain
25	chr18:13301800-13303000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr18:13301800-13303000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr18:13301800-13303200	Enhancers	Rectal Smooth Muscle	rectum
28	chr18:13301800-13303400	Enhancers	Fetal Lung	lung
29	chr18:13301800-13303400	Enhancers	Fetal Stomach	stomach
30	chr18:13301800-13303600	Enhancers	Colon Smooth Muscle	Colon
31	chr18:13301800-13304000	Enhancers	Thymus	Thymus
32	chr18:13301800-13304200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr18:13301800-13304600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr18:13301800-13305800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:13302000-13302800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr18:13302000-13302800	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr18:13302000-13303000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr18:13302000-13303000	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr18:13302000-13303000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr18:13302000-13303000	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr18:13302000-13303000	Enhancers	Liver	Liver
42	chr18:13302000-13303000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr18:13302000-13303000	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr18:13302000-13304400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr18:13302000-13305000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr18:13302200-13303000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr18:13302200-13303000	Flanking Active TSS	Fetal Brain Female	brain
48	chr18:13302200-13303200	Enhancers	Psoas Muscle	Psoas
49	chr18:13302200-13303600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr18:13302200-13303600	Enhancers	Adipose Nuclei	Adipose

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