Variant report

Variant	rs1430780
Chromosome Location	chr2:67878328-67878329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:67464250..67465118-chr2:67877852..67878567,2	MCF-7	breast:
2	chr2:67871857..67874448-chr2:67877443..67879298,2	K562	blood:
3	chr2:67877825..67878403-chr5:28935689..28936434,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11126146	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11675008	0.82[ASN][1000 genomes]
rs11692071	0.82[ASN][1000 genomes]
rs13418956	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1367473	0.90[ASN][1000 genomes]
rs1430779	0.97[ASN][1000 genomes]
rs1430781	0.90[ASN][1000 genomes]
rs1430782	0.88[ASN][1000 genomes]
rs6737368	0.82[ASN][1000 genomes]
rs6749904	0.90[ASN][1000 genomes]
rs9712235	0.81[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	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv1007345	chr2:67870225-67980094	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1430780	APLF	cis	cerebellum	SCAN
rs1430780	ACTR2	cis	cerebellum	SCAN
rs1430780	APLF	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67866800-67884200	Weak transcription	Aorta	Aorta
2	chr2:67875000-67878400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:67875200-67879000	Enhancers	Hela-S3	cervix
4	chr2:67875200-67879200	Enhancers	Fetal Stomach	stomach
5	chr2:67875600-67878800	Enhancers	Adipose Nuclei	Adipose
6	chr2:67876200-67878400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:67876200-67878800	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:67876200-67879000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:67876200-67879000	Enhancers	Colon Smooth Muscle	Colon
10	chr2:67876200-67879000	Enhancers	Fetal Muscle Leg	muscle
11	chr2:67876200-67879000	Enhancers	Ovary	ovary
12	chr2:67876200-67879200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:67876400-67878400	Enhancers	Fetal Muscle Trunk	muscle
14	chr2:67876400-67878800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:67876400-67878800	Enhancers	A549	lung
16	chr2:67876400-67878800	Enhancers	HSMM	muscle
17	chr2:67876400-67879000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:67876400-67879000	Enhancers	NHDF-Ad	bronchial
19	chr2:67876400-67879400	Enhancers	Brain Germinal Matrix	brain
20	chr2:67876600-67879000	Enhancers	HSMMtube	muscle
21	chr2:67876600-67879000	Enhancers	NH-A	brain
22	chr2:67876800-67878600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:67876800-67878800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr2:67876800-67878800	Bivalent Enhancer	Fetal Intestine Small	intestine
25	chr2:67877200-67878400	Enhancers	Fetal Brain Female	brain
26	chr2:67877200-67878400	Enhancers	Fetal Intestine Large	intestine
27	chr2:67877200-67878400	Weak transcription	Fetal Kidney	kidney
28	chr2:67877200-67879000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:67877200-67879600	Enhancers	Fetal Lung	lung
30	chr2:67877400-67878400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:67877400-67878600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:67877400-67878600	Weak transcription	Right Ventricle	heart
33	chr2:67877400-67878800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr2:67877400-67879000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:67877600-67878600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:67877800-67878400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:67877800-67878400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:67877800-67878400	Active TSS	Stomach Smooth Muscle	stomach
39	chr2:67877800-67878800	Enhancers	Osteobl	bone
40	chr2:67878000-67878400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:67878000-67878400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:67878000-67878400	Enhancers	NHLF	lung
43	chr2:67878000-67879000	Enhancers	Fetal Heart	heart
44	chr2:67878200-67878400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr2:67878200-67878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:67878200-67878400	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr2:67878200-67878400	Enhancers	Left Ventricle	heart
48	chr2:67878200-67878400	Enhancers	Psoas Muscle	Psoas
49	chr2:67878200-67878600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:67878200-67878600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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