Variant report

Variant	rs10502421
Chromosome Location	chr18:13464437-13464438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr18:13464425-13465295	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13461836..13465101-chr18:13470450..13473668,3	MCF-7	breast:

Variant related genes	Relation type
LDLRAD4	TF binding region
ENSG00000267694	Chromatin interaction
ENSG00000267529	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6505815	0.83[EUR][1000 genomes]
rs8087070	0.83[ASN][1000 genomes]
rs8089773	0.90[CHD][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv909411	chr18:13425604-13493554	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10502421	PPP4R1	cis	cerebellum	SCAN
rs10502421	C18orf1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13452400-13464800	Weak transcription	Colonic Mucosa	Colon
2	chr18:13453000-13464800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr18:13453000-13494800	Weak transcription	Aorta	Aorta
4	chr18:13456400-13464800	Weak transcription	Spleen	Spleen
5	chr18:13456400-13467200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:13456600-13497800	Weak transcription	Gastric	stomach
7	chr18:13457400-13470400	Weak transcription	Fetal Heart	heart
8	chr18:13458800-13465400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr18:13459000-13465000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr18:13459200-13464600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr18:13460200-13465000	Weak transcription	HepG2	liver
12	chr18:13460800-13464600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr18:13460800-13464800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr18:13461000-13465000	Enhancers	Primary hematopoietic stem cells	blood
15	chr18:13461000-13465800	Enhancers	Fetal Brain Male	brain
16	chr18:13461400-13464800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:13461800-13464600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr18:13461800-13464800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr18:13462200-13464600	Enhancers	Primary B cells from peripheral blood	blood
20	chr18:13462200-13464600	Enhancers	Brain Germinal Matrix	brain
21	chr18:13462200-13465600	Weak transcription	Psoas Muscle	Psoas
22	chr18:13462400-13464800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr18:13462400-13465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr18:13462800-13464600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr18:13463000-13465000	Enhancers	Brain Anterior Caudate	brain
26	chr18:13463200-13464600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr18:13463200-13464600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr18:13463200-13464600	Enhancers	Brain Angular Gyrus	brain
29	chr18:13463200-13464600	Enhancers	Fetal Thymus	thymus
30	chr18:13463200-13465000	Enhancers	Brain Hippocampus Middle	brain
31	chr18:13463200-13465600	Enhancers	Brain Cingulate Gyrus	brain
32	chr18:13463200-13470400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr18:13463400-13464600	Enhancers	Adipose Nuclei	Adipose
34	chr18:13463400-13464800	Weak transcription	Right Ventricle	heart
35	chr18:13463400-13465000	Weak transcription	Right Atrium	heart
36	chr18:13463400-13465600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr18:13463400-13465800	Enhancers	Fetal Brain Female	brain
38	chr18:13463400-13466800	Weak transcription	Small Intestine	intestine
39	chr18:13463400-13470600	Weak transcription	Pancreas	Pancrea
40	chr18:13463400-13470800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr18:13463600-13464800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr18:13463600-13465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr18:13463600-13465000	Enhancers	HUVEC	blood vessel
44	chr18:13463600-13465400	Flanking Active TSS	Dnd41	blood
45	chr18:13463800-13464600	Weak transcription	Placenta	Placenta
46	chr18:13463800-13464800	Weak transcription	Fetal Muscle Leg	muscle
47	chr18:13463800-13464800	Weak transcription	Left Ventricle	heart
48	chr18:13463800-13471200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr18:13464000-13464800	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr18:13464000-13464800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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