Variant report

Variant	rs9843001
Chromosome Location	chr3:119052591-119052592
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119041710..119043371-chr3:119051543..119054199,2	K562	blood:
2	chr3:119045537..119049626-chr3:119052248..119055183,4	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11918598	0.81[JPT][hapmap]
rs17281577	0.81[JPT][hapmap]
rs2044621	0.84[CEU][hapmap]
rs58374436	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6784281	0.81[EUR][1000 genomes]
rs72962562	0.88[ASN][1000 genomes]
rs9835104	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863675	0.84[CEU][hapmap]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9843001	TMEM39A	cis	parietal	SCAN
rs9843001	IQCB1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119042600-119054000	Weak transcription	NHLF	lung
2	chr3:119042600-119055600	Weak transcription	Fetal Brain Male	brain
3	chr3:119042800-119052800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:119042800-119053000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:119042800-119056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119042800-119070600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:119042800-119072000	Weak transcription	Thymus	Thymus
8	chr3:119043000-119069000	Weak transcription	Primary T cells from cord blood	blood
9	chr3:119043200-119062400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:119046000-119052800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:119046000-119056000	Weak transcription	Fetal Thymus	thymus
12	chr3:119046000-119064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:119046000-119064600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:119046800-119056000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:119047000-119053800	Enhancers	Fetal Stomach	stomach
16	chr3:119047800-119053600	Enhancers	Ovary	ovary
17	chr3:119048000-119054600	Enhancers	Fetal Heart	heart
18	chr3:119048800-119052800	Weak transcription	Colonic Mucosa	Colon
19	chr3:119048800-119062800	Weak transcription	Osteobl	bone
20	chr3:119049000-119052800	Weak transcription	Brain Germinal Matrix	brain
21	chr3:119049200-119052600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:119049200-119062200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:119049200-119071200	Weak transcription	Aorta	Aorta
24	chr3:119049400-119052600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr3:119049400-119052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:119049400-119056000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:119049600-119068000	Weak transcription	NH-A	brain
28	chr3:119050000-119052800	Weak transcription	Right Ventricle	heart
29	chr3:119050000-119062000	Weak transcription	Placenta	Placenta
30	chr3:119050400-119053600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:119050400-119053800	Enhancers	Adipose Nuclei	Adipose
32	chr3:119050600-119053800	Enhancers	Stomach Smooth Muscle	stomach
33	chr3:119050800-119052800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:119050800-119052800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:119050800-119053000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:119050800-119056000	Weak transcription	HSMM	muscle
37	chr3:119050800-119064600	Weak transcription	HSMMtube	muscle
38	chr3:119050800-119075800	Weak transcription	Pancreas	Pancrea
39	chr3:119051000-119053200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:119051000-119053200	Weak transcription	Psoas Muscle	Psoas
41	chr3:119051000-119055400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:119051000-119064800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:119051200-119053200	Enhancers	Fetal Muscle Leg	muscle
44	chr3:119051400-119052600	Enhancers	Brain Substantia Nigra	brain
45	chr3:119051400-119052800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:119051400-119053600	Enhancers	Fetal Lung	lung
47	chr3:119051600-119052600	Enhancers	K562	blood
48	chr3:119051800-119053800	Enhancers	Right Atrium	heart
49	chr3:119051800-119054600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:119051800-119056000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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