Variant report

Variant	rs12963130
Chromosome Location	chr18:13297966-13297967
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	chr18:13297804..13299921-chr18:13302909..13305321,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11659839	0.89[EUR][1000 genomes]
rs11659895	0.83[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12458323	0.80[EUR][1000 genomes]
rs12967286	1.00[JPT][hapmap]
rs4797759	1.00[JPT][hapmap]
rs62097350	0.89[EUR][1000 genomes]
rs6505797	1.00[JPT][hapmap]
rs8084225	0.92[CEU][hapmap]
rs9947965	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12963130	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13274600-13301600	Weak transcription	Brain Substantia Nigra	brain
2	chr18:13274600-13302400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr18:13280800-13299800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:13282800-13301600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr18:13285000-13316200	Weak transcription	Aorta	Aorta
6	chr18:13285400-13302600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr18:13287200-13298000	Weak transcription	Spleen	Spleen
8	chr18:13290000-13301800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr18:13291600-13299800	Weak transcription	Pancreas	Pancrea
10	chr18:13291600-13302000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr18:13292200-13300000	Weak transcription	Adipose Nuclei	Adipose
12	chr18:13292400-13299800	Weak transcription	Right Atrium	heart
13	chr18:13292400-13302000	Weak transcription	Liver	Liver
14	chr18:13293000-13300000	Weak transcription	Fetal Brain Female	brain
15	chr18:13293000-13301800	Weak transcription	Fetal Stomach	stomach
16	chr18:13293200-13300200	Weak transcription	Brain Anterior Caudate	brain
17	chr18:13294400-13298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr18:13294400-13299800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr18:13294400-13299800	Weak transcription	Fetal Muscle Leg	muscle
20	chr18:13294400-13300000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr18:13294400-13300000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr18:13294600-13300000	Weak transcription	Psoas Muscle	Psoas
23	chr18:13294800-13298200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:13295200-13299200	Weak transcription	Fetal Heart	heart
25	chr18:13295600-13312600	Weak transcription	Dnd41	blood
26	chr18:13296600-13298800	Enhancers	Right Ventricle	heart
27	chr18:13296600-13301200	Genic enhancers	Fetal Thymus	thymus
28	chr18:13296600-13301400	Weak transcription	Brain Angular Gyrus	brain
29	chr18:13297200-13298200	Weak transcription	Lung	lung
30	chr18:13297400-13298000	Weak transcription	Left Ventricle	heart
31	chr18:13297400-13302000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr18:13297600-13302000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr18:13297600-13302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr18:13297600-13302400	Weak transcription	Primary T cells from cord blood	blood
35	chr18:13297800-13301800	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr18:13297800-13301800	Genic enhancers	Thymus	Thymus

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