Variant report

Variant	rs4788414
Chromosome Location	chr16:30434160-30434161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30433604-30434311	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30432578..30437001-chr16:30438617..30442796,8	MCF-7	breast:
2	chr16:30427085..30432529-chr16:30433296..30438861,8	MCF-7	breast:
3	chr16:30433382..30435767-chr16:30438865..30440631,2	K562	blood:

Variant related genes	Relation type
ENSG00000199787	TF binding region
ENSG00000179958	Chromatin interaction
ENSG00000199787	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11150586	0.84[EUR][1000 genomes]
rs11640950	0.86[ASN][1000 genomes]
rs11642676	0.81[EUR][1000 genomes]
rs11646130	0.81[EUR][1000 genomes]
rs12165013	0.86[EUR][1000 genomes]
rs12446288	0.81[EUR][1000 genomes]
rs12447833	0.85[EUR][1000 genomes]
rs12921440	0.82[EUR][1000 genomes]
rs13333093	0.82[EUR][1000 genomes]
rs35598865	0.92[ASN][1000 genomes]
rs3574	0.82[EUR][1000 genomes]
rs4465620	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4787643	0.85[EUR][1000 genomes]
rs4788409	0.85[EUR][1000 genomes]
rs4788413	0.92[EUR][1000 genomes]
rs62055459	0.85[EUR][1000 genomes]
rs6565182	0.82[EUR][1000 genomes]
rs7203359	0.86[EUR][1000 genomes]
rs73532600	0.82[EUR][1000 genomes]
rs8046445	0.80[EUR][1000 genomes]
rs8060853	0.88[EUR][1000 genomes]
rs9888967	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4788414	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs4788414	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30421200-30437600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:30421200-30437600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:30428800-30440200	Weak transcription	Fetal Heart	heart
4	chr16:30429200-30435000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:30429600-30440200	Weak transcription	NHDF-Ad	bronchial
6	chr16:30429800-30434800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr16:30429800-30434800	Weak transcription	Ovary	ovary
8	chr16:30429800-30435000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr16:30429800-30435400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:30429800-30440200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr16:30429800-30440200	Weak transcription	Fetal Kidney	kidney
12	chr16:30429800-30440200	Weak transcription	HSMMtube	muscle
13	chr16:30429800-30440400	Weak transcription	Right Atrium	heart
14	chr16:30430000-30434800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:30430000-30434800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr16:30430000-30435000	Weak transcription	Brain Angular Gyrus	brain
17	chr16:30430000-30435000	Weak transcription	NH-A	brain
18	chr16:30430000-30435200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:30430000-30437200	Weak transcription	Brain Substantia Nigra	brain
20	chr16:30430000-30439400	Weak transcription	Fetal Brain Male	brain
21	chr16:30430000-30440200	Strong transcription	Fetal Intestine Small	intestine
22	chr16:30430000-30440400	Weak transcription	Small Intestine	intestine
23	chr16:30430000-30440600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr16:30430200-30434800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr16:30430200-30434800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr16:30430200-30434800	Weak transcription	Colonic Mucosa	Colon
27	chr16:30430200-30435000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr16:30430200-30435000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr16:30430200-30435000	Weak transcription	Brain Anterior Caudate	brain
30	chr16:30430200-30435000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:30430200-30435000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr16:30430200-30435000	Weak transcription	HUVEC	blood vessel
33	chr16:30430200-30435200	Weak transcription	Pancreas	Pancrea
34	chr16:30430200-30435600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr16:30430200-30438800	Weak transcription	Colon Smooth Muscle	Colon
36	chr16:30430200-30440000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr16:30430200-30440000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr16:30430200-30440200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:30430200-30440200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr16:30430200-30440600	Weak transcription	Psoas Muscle	Psoas
41	chr16:30430400-30434600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr16:30430400-30434800	Weak transcription	Gastric	stomach
43	chr16:30430400-30439000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr16:30430600-30439400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr16:30430600-30440200	Strong transcription	Fetal Stomach	stomach
46	chr16:30430600-30440400	Weak transcription	Stomach Mucosa	stomach
47	chr16:30431400-30436800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr16:30431400-30437400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr16:30431600-30436200	Strong transcription	Fetal Intestine Large	intestine
50	chr16:30431600-30436200	Strong transcription	Right Ventricle	heart

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