Variant report

Variant	rs11659895
Chromosome Location	chr18:13301705-13301706
allele	C/T
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: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11659839	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11663785	1.00[JPT][hapmap]
rs12458323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963130	0.83[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1893978	0.80[CEU][hapmap]
rs1893979	0.80[CEU][hapmap]
rs62096867	0.81[EUR][1000 genomes]
rs62097350	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9960998	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3427325	chr18:13301605-13301866	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11659895	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:53 , 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	chr18:13290000-13301800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr18:13291600-13302000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr18:13292400-13302000	Weak transcription	Liver	Liver
7	chr18:13293000-13301800	Weak transcription	Fetal Stomach	stomach
8	chr18:13295600-13312600	Weak transcription	Dnd41	blood
9	chr18:13297400-13302000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr18:13297600-13302000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr18:13297600-13302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr18:13297600-13302400	Weak transcription	Primary T cells from cord blood	blood
13	chr18:13297800-13301800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr18:13297800-13301800	Genic enhancers	Thymus	Thymus
15	chr18:13298600-13303000	Weak transcription	Gastric	stomach
16	chr18:13298800-13302600	Enhancers	Fetal Brain Male	brain
17	chr18:13298800-13303400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:13298800-13314600	Weak transcription	Fetal Intestine Small	intestine
19	chr18:13299200-13302200	Enhancers	Fetal Heart	heart
20	chr18:13299800-13302000	Enhancers	Fetal Muscle Trunk	muscle
21	chr18:13299800-13302200	Enhancers	Right Atrium	heart
22	chr18:13299800-13303200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr18:13299800-13303400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr18:13299800-13304200	Enhancers	Fetal Muscle Leg	muscle
25	chr18:13299800-13304600	Enhancers	Left Ventricle	heart
26	chr18:13300000-13302200	Enhancers	Fetal Brain Female	brain
27	chr18:13300000-13303200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr18:13300000-13303400	Enhancers	Right Ventricle	heart
29	chr18:13300200-13302000	Enhancers	Brain Anterior Caudate	brain
30	chr18:13300400-13304400	Weak transcription	Pancreas	Pancrea
31	chr18:13300600-13301800	Weak transcription	HSMMtube	muscle
32	chr18:13300600-13302200	Weak transcription	Adipose Nuclei	Adipose
33	chr18:13300600-13302600	Weak transcription	Lung	lung
34	chr18:13300800-13301800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr18:13301200-13302200	Weak transcription	Psoas Muscle	Psoas
36	chr18:13301200-13302400	Weak transcription	Spleen	Spleen
37	chr18:13301200-13304400	Enhancers	Fetal Thymus	thymus
38	chr18:13301200-13308400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr18:13301400-13303200	Enhancers	Brain Angular Gyrus	brain
40	chr18:13301400-13303600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:13301400-13304000	Enhancers	Brain Germinal Matrix	brain
42	chr18:13301600-13301800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr18:13301600-13302200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:13301600-13302400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr18:13301600-13302600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr18:13301600-13302600	Enhancers	Fetal Kidney	kidney
47	chr18:13301600-13302800	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr18:13301600-13303000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr18:13301600-13303400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr18:13301600-13304000	Enhancers	Brain Substantia Nigra	brain

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