Variant report

Variant	rs1562788
Chromosome Location	chr3:150065903-150065904
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150058583..150074355-chr3:150124068..150134356,51	MCF-7	breast:
2	chr3:150063831..150066264-chr3:150212112..150214058,2	MCF-7	breast:
3	chr3:149955913..149960046-chr3:150062431..150067841,6	MCF-7	breast:
4	chr3:149965841..149967659-chr3:150065156..150067376,2	MCF-7	breast:
5	chr3:150024822..150026384-chr3:150064779..150066444,2	MCF-7	breast:
6	chr3:150064599..150068049-chr3:150092339..150097012,5	MCF-7	breast:
7	chr3:150064573..150066847-chr3:150070283..150072225,2	K562	blood:
8	chr3:150059766..150072041-chr3:150122033..150133129,50	MCF-7	breast:
9	chr3:150064573..150066917-chr3:150070283..150073113,2	K562	blood:
10	chr3:150061806..150067641-chr3:150085085..150089827,11	MCF-7	breast:
11	chr3:150064216..150066943-chr3:150260287..150264340,3	MCF-7	breast:
12	chr11:1753546..1755772-chr3:150063275..150066246,2	MCF-7	breast:
13	chr3:150023976..150025654-chr3:150064585..150066377,2	MCF-7	breast:
14	chr3:149944451..149946026-chr3:150065716..150067685,2	MCF-7	breast:
15	chr3:150028795..150040018-chr3:150059749..150069074,18	MCF-7	breast:
16	chr3:149954224..149957668-chr3:150065755..150069170,3	MCF-7	breast:
17	chr3:150033272..150039330-chr3:150061780..150068166,12	MCF-7	breast:
18	chr3:150063392..150066331-chr3:150098048..150099992,2	MCF-7	breast:
19	chr3:150047065..150050412-chr3:150064915..150067808,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244541	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16862607	1.00[CHB][hapmap]
rs2060662	1.00[CHB][hapmap]
rs2868429	1.00[JPT][hapmap]
rs4533673	1.00[ASN][1000 genomes]
rs4681623	1.00[ASN][1000 genomes]
rs62271371	1.00[ASN][1000 genomes]
rs6767155	1.00[CHB][hapmap]
rs73162478	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617699	1.00[CHB][hapmap]
rs7636643	1.00[CHB][hapmap]
rs9836480	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9862778	1.00[CHB][hapmap]

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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1562788	RNF13	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150053000-150066600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:150058200-150067600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:150058400-150066000	Weak transcription	Aorta	Aorta
4	chr3:150058400-150067400	Weak transcription	Right Atrium	heart
5	chr3:150060800-150067400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:150060800-150067400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:150061800-150071000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:150061800-150071000	Enhancers	HMEC	breast
9	chr3:150062600-150067600	Weak transcription	Fetal Stomach	stomach
10	chr3:150062800-150068000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:150063200-150066600	Enhancers	Hela-S3	cervix
12	chr3:150063400-150066000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:150063400-150067800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:150064000-150066200	Flanking Active TSS	NHDF-Ad	bronchial
15	chr3:150064000-150066600	Enhancers	HSMM	muscle
16	chr3:150064200-150066200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:150064200-150066400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:150064200-150068000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:150064400-150066200	Enhancers	NH-A	brain
20	chr3:150064400-150066400	Flanking Active TSS	A549	lung
21	chr3:150064400-150066800	Enhancers	Fetal Heart	heart
22	chr3:150064400-150067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:150064400-150069400	Enhancers	HSMMtube	muscle
24	chr3:150064600-150066200	Flanking Active TSS	NHEK	skin
25	chr3:150064600-150067400	Enhancers	NHLF	lung
26	chr3:150064800-150068000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:150064800-150068000	Enhancers	Adipose Nuclei	Adipose
28	chr3:150064800-150068600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:150065000-150066000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:150065000-150066200	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr3:150065000-150066600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:150065000-150068800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:150065200-150066000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:150065200-150066000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:150065200-150066600	Enhancers	Osteobl	bone
36	chr3:150065200-150067600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:150065200-150068000	Enhancers	Colon Smooth Muscle	Colon
38	chr3:150065200-150068000	Enhancers	Rectal Smooth Muscle	rectum
39	chr3:150065200-150068000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:150065200-150068600	Enhancers	Fetal Muscle Leg	muscle
41	chr3:150065200-150069200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:150065200-150069600	Enhancers	HUVEC	blood vessel
43	chr3:150065200-150072600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:150065400-150067400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:150065400-150068200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:150065400-150071000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:150065400-150072600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:150065600-150066600	Weak transcription	Brain Anterior Caudate	brain
49	chr3:150065600-150067600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:150065600-150067600	Weak transcription	Stomach Smooth Muscle	stomach

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