Variant report

Variant	rs4858794
Chromosome Location	chr3:48490193-48490194
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48489623-48490307	HepG2	liver:	n/a	n/a
2	STAT3	chr3:48490176-48490275	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48487745..48490928-chr3:48507452..48510660,3	K562	blood:
2	chr3:48488969..48490490-chr3:48600072..48601690,2	K562	blood:
3	chr3:48489931..48491673-chr3:48592695..48595764,3	K562	blood:
4	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
5	chr3:48489543..48493797-chr3:48496122..48499063,3	MCF-7	breast:
6	chr3:48490070..48492746-chr3:48498411..48500259,2	MCF-7	breast:
7	chr3:48463922..48465438-chr3:48487948..48490682,2	MCF-7	breast:
8	chr3:48487008..48490928-chr3:48507402..48510491,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244380	TF binding region
ENSG00000213689	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000145040	Chromatin interaction
ENSG00000114268	Chromatin interaction

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

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

rs_ID	r²[population]
rs4075800	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs56073014	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6442128	0.85[AFR][1000 genomes]
rs6783952	0.89[AFR][1000 genomes]
rs6786152	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6807104	0.85[AFR][1000 genomes]
rs7630353	1.00[MEX][hapmap]
rs9866124	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858794	SHISA5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48489000-48492000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:48489000-48492800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:48489000-48492800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:48489000-48492800	Weak transcription	Left Ventricle	heart
5	chr3:48489000-48493200	Weak transcription	Ovary	ovary
6	chr3:48489000-48494400	Weak transcription	Aorta	Aorta
7	chr3:48489200-48490400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:48489200-48491400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:48489200-48492000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:48489200-48492400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:48489200-48492400	Weak transcription	Lung	lung
12	chr3:48489200-48492600	Weak transcription	Primary T cells from cord blood	blood
13	chr3:48489200-48492600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:48489200-48492600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:48489200-48492800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:48489200-48493000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:48489200-48494400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:48489200-48494400	Weak transcription	Esophagus	oesophagus
19	chr3:48489200-48494600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:48489200-48494800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:48489200-48498800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:48489200-48506200	Weak transcription	Stomach Mucosa	stomach
23	chr3:48489200-48507400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:48489400-48490400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:48489400-48490400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:48489400-48490400	Enhancers	Brain Germinal Matrix	brain
27	chr3:48489400-48490400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:48489400-48490400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:48489400-48490400	Enhancers	HepG2	liver
30	chr3:48489400-48491400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:48489400-48491400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:48489400-48491800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:48489400-48492000	Weak transcription	Liver	Liver
34	chr3:48489400-48492000	Weak transcription	Placenta	Placenta
35	chr3:48489400-48492400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:48489400-48492400	Weak transcription	Fetal Brain Female	brain
37	chr3:48489400-48492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:48489400-48492600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:48489400-48492600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:48489400-48492600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:48489400-48492600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:48489400-48492600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:48489400-48492600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:48489400-48492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:48489400-48492800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:48489400-48492800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:48489400-48492800	Weak transcription	Brain Anterior Caudate	brain
48	chr3:48489400-48492800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr3:48489400-48492800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:48489400-48492800	Weak transcription	Duodenum Mucosa	Duodenum

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