Variant report

Variant	rs30384
Chromosome Location	chr5:179295060-179295061
allele	A/G
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	USF1	chr5:179294994-179295182	HepG2	liver:	n/a	chr5:179295092-179295103
2	POLR2A	chr5:179294351-179295111	SK-N-MC	brain:	n/a	n/a
3	USF1	chr5:179294948-179295191	H1-hESC	embryonic stem cell:	n/a	chr5:179295092-179295103
4	ZNF384	chr5:179295028-179295135	K562	blood:	n/a	n/a
5	USF1	chr5:179294996-179295145	SK-N-SH_RA	brain:	n/a	chr5:179295092-179295103
6	POLR2A	chr5:179294796-179295119	K562	blood:	n/a	n/a
7	USF1	chr5:179294945-179295216	H1-hESC	embryonic stem cell:	n/a	chr5:179295092-179295103
8	USF1	chr5:179294956-179295194	SK-N-SH_RA	brain:	n/a	chr5:179295092-179295103
9	USF1	chr5:179294935-179295183	K562	blood:	n/a	chr5:179295092-179295103
10	USF1	chr5:179294953-179295174	ECC-1	luminal epithelium:	n/a	chr5:179295092-179295103
11	USF1	chr5:179294906-179295207	SK-N-SH	brain:	n/a	chr5:179295092-179295103
12	USF1	chr5:179294949-179295184	K562	blood:	n/a	chr5:179295092-179295103
13	POLR2A	chr5:179294785-179295204	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179294097..179296495-chr5:179297933..179301525,5	K562	blood:
2	chr5:179288312..179290452-chr5:179293485..179295109,2	MCF-7	breast:
3	chr5:179285116..179287409-chr5:179295017..179296656,2	MCF-7	breast:
4	chr5:179252835..179255633-chr5:179294547..179297235,2	K562	blood:
5	chr5:179289788..179295879-chr5:179298486..179302200,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf45-1	chr5:179295058-179296834	NONHSAT105652

Variant related genes	Relation type
TBC1D9B	TF binding region
ENSG00000245317	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000161010	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10073754	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193714	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248253	0.85[CEU][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs27744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32460	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs32462	0.86[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats 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	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
9	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
11	nsv883286	chr5:179290845-179313656	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs30384	HIGD2A	cis	cerebellum	SCAN
rs30384	C5orf45	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179286200-179310600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179286400-179303000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:179287200-179296400	Weak transcription	HUVEC	blood vessel
7	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
8	chr5:179287800-179296800	Weak transcription	Fetal Heart	heart
9	chr5:179287800-179302200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:179287800-179310000	Weak transcription	Fetal Brain Male	brain
11	chr5:179288400-179308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:179288400-179308400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:179289000-179295200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:179289000-179295200	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr5:179289000-179300400	Strong transcription	Osteobl	bone
17	chr5:179289000-179306800	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr5:179289000-179307000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:179289000-179308800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:179289000-179309200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:179289200-179295800	Strong transcription	Fetal Thymus	thymus
22	chr5:179289200-179297600	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:179289200-179297800	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:179289200-179303400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:179289200-179303800	Strong transcription	Pancreas	Pancrea
26	chr5:179289200-179305000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:179289200-179307000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:179289200-179307800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:179289200-179308600	Strong transcription	Liver	Liver
30	chr5:179289200-179308600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:179289200-179308800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:179289200-179309200	Strong transcription	Fetal Brain Female	brain
33	chr5:179289400-179296000	Strong transcription	Right Ventricle	heart
34	chr5:179289400-179297800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr5:179289400-179306800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:179289400-179307400	Strong transcription	Primary T cells from cord blood	blood
37	chr5:179289400-179307600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr5:179289400-179308200	Strong transcription	Dnd41	blood
39	chr5:179289400-179308400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:179289400-179308400	Strong transcription	Ovary	ovary
41	chr5:179289400-179308400	Strong transcription	Stomach Smooth Muscle	stomach
42	chr5:179289400-179308400	Strong transcription	Thymus	Thymus
43	chr5:179289400-179309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:179289600-179303000	Strong transcription	Colonic Mucosa	Colon
45	chr5:179289600-179308800	Strong transcription	Brain Germinal Matrix	brain
46	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
47	chr5:179289800-179296000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:179289800-179296200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr5:179289800-179301000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:179289800-179303800	Strong transcription	NHLF	lung

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