Variant report

Variant	rs1394763
Chromosome Location	chr3:24393296-24393297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24388234..24394796-chr3:24535666..24539509,6	K562	blood:
2	chr3:24232065..24234894-chr3:24391713..24393801,2	K562	blood:
3	chr3:24382041..24384823-chr3:24392425..24394516,2	K562	blood:
4	chr3:24383601..24387139-chr3:24393091..24396535,3	MCF-7	breast:
5	chr3:24382413..24383987-chr3:24390785..24393314,2	MCF-7	breast:
6	chr3:24392934..24395515-chr3:24399959..24401647,2	K562	blood:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1354599	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1354600	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs17014547	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17014561	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs59263745	0.98[AFR][1000 genomes]
rs73043725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043737	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825626	0.98[AFR][1000 genomes]
rs73825627	0.89[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1394763	ARMCX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24360400-24418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:24381000-24394800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:24390400-24401000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:24391000-24398600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:24391200-24401000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:24392400-24393400	Flanking Active TSS	K562	blood
7	chr3:24392600-24394800	Enhancers	Colon Smooth Muscle	Colon
8	chr3:24392800-24393600	Enhancers	Brain Cingulate Gyrus	brain
9	chr3:24392800-24394200	Enhancers	Adipose Nuclei	Adipose
10	chr3:24392800-24394400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:24392800-24394600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:24392800-24395000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:24392800-24396400	Enhancers	Liver	Liver
14	chr3:24392800-24396400	Enhancers	HepG2	liver
15	chr3:24393000-24394000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:24393000-24394000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:24393000-24394000	Enhancers	HMEC	breast
18	chr3:24393000-24394400	Enhancers	Fetal Intestine Large	intestine
19	chr3:24393000-24394600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr3:24393000-24394800	Enhancers	Brain Substantia Nigra	brain
21	chr3:24393000-24395000	Enhancers	Fetal Lung	lung
22	chr3:24393000-24395200	Enhancers	Psoas Muscle	Psoas
23	chr3:24393200-24393400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:24393200-24393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:24393200-24393400	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr3:24393200-24393600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:24393200-24393600	Enhancers	Aorta	Aorta
28	chr3:24393200-24393600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr3:24393200-24393600	Enhancers	Stomach Mucosa	stomach
30	chr3:24393200-24393600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr3:24393200-24393800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr3:24393200-24394000	Enhancers	Brain Angular Gyrus	brain
33	chr3:24393200-24394000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:24393200-24394000	Enhancers	Fetal Stomach	stomach
35	chr3:24393200-24394000	Enhancers	Gastric	stomach
36	chr3:24393200-24394000	Enhancers	Left Ventricle	heart
37	chr3:24393200-24394000	Enhancers	Ovary	ovary
38	chr3:24393200-24394000	Enhancers	Pancreas	Pancrea
39	chr3:24393200-24394000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:24393200-24394000	Enhancers	Right Atrium	heart
41	chr3:24393200-24394000	Enhancers	Right Ventricle	heart
42	chr3:24393200-24394000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr3:24393200-24394000	Enhancers	Small Intestine	intestine
44	chr3:24393200-24394000	Enhancers	NHLF	lung
45	chr3:24393200-24394400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:24393200-24394800	Enhancers	Brain Hippocampus Middle	brain
47	chr3:24393200-24395400	Enhancers	Fetal Intestine Small	intestine

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