Variant report

Variant	rs30385
Chromosome Location	chr5:179292010-179292011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179291960-179292180	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:179291665-179292085	K562	blood:	n/a	n/a
3	POLR2A	chr5:179291803-179292694	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179285301..179288103-chr5:179290972..179294711,5	MCF-7	breast:
2	chr5:179290999..179292757-chr5:179334523..179336715,2	K562	blood:
3	chr5:179232974..179236015-chr5:179291213..179293489,3	K562	blood:
4	chr5:179247857..179250195-chr5:179290932..179292634,3	K562	blood:
5	chr5:179290040..179292104-chr5:179300801..179303635,2	K562	blood:
6	chr5:179230087..179232097-chr5:179290171..179292438,2	K562	blood:
7	chr5:179288562..179291092-chr5:179291407..179293097,2	MCF-7	breast:
8	chr5:179290591..179292919-chr5:179305616..179307506,2	MCF-7	breast:
9	chr5:179289788..179295879-chr5:179298486..179302200,7	MCF-7	breast:
10	chr5:179290493..179292247-chr5:179297016..179298960,2	K562	blood:
11	chr5:179284411..179288482-chr5:179291303..179294641,8	MCF-7	breast:

No data

Variant related genes	Relation type
C5orf45	TF binding region
ENSG00000161013	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs152233	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152236	0.82[ASN][1000 genomes]
rs152237	0.82[ASN][1000 genomes]
rs152238	0.82[ASN][1000 genomes]
rs155791	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs155795	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs155796	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs155797	0.84[ASN][1000 genomes]
rs156101	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs156104	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1684973	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs182086	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431123	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2431124	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434411	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248218	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248219	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248222	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248232	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs248252	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26074	0.81[ASN][1000 genomes]
rs26075	0.81[EUR][1000 genomes]
rs26078	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27410	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27411	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27471	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs27474	0.80[ASN][1000 genomes]
rs28325	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30381	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30382	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32437	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32438	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32461	0.91[ASN][1000 genomes]
rs32469	0.81[ASN][1000 genomes]
rs32470	0.81[ASN][1000 genomes]
rs32471	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32472	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734003	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs43155	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs532795	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574997	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs578659	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs860706	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs88183	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9957	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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
rs30385	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL
rs30385	TBC1D9B	cis	Muscle Skeletal	GTEx

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	chr5:179287400-179294600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:179287800-179296800	Weak transcription	Fetal Heart	heart
10	chr5:179287800-179302200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:179287800-179310000	Weak transcription	Fetal Brain Male	brain
12	chr5:179288400-179292400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:179288400-179292400	Strong transcription	HSMM	muscle
14	chr5:179288400-179308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:179288400-179308400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:179288800-179292400	Strong transcription	A549	lung
18	chr5:179289000-179294200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:179289000-179294400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:179289000-179294600	Strong transcription	Fetal Lung	lung
21	chr5:179289000-179295200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:179289000-179295200	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr5:179289000-179300400	Strong transcription	Osteobl	bone
24	chr5:179289000-179306800	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr5:179289000-179307000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:179289000-179308800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:179289000-179309200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:179289200-179292600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:179289200-179292800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:179289200-179293200	Strong transcription	Spleen	Spleen
31	chr5:179289200-179294000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:179289200-179294000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:179289200-179294000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:179289200-179294200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr5:179289200-179294200	Strong transcription	NHEK	skin
36	chr5:179289200-179294800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr5:179289200-179295800	Strong transcription	Fetal Thymus	thymus
38	chr5:179289200-179297600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:179289200-179297800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:179289200-179303400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:179289200-179303800	Strong transcription	Pancreas	Pancrea
42	chr5:179289200-179305000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:179289200-179307000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:179289200-179307800	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:179289200-179308600	Strong transcription	Liver	Liver
46	chr5:179289200-179308600	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:179289200-179308800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:179289200-179309200	Strong transcription	Fetal Brain Female	brain
49	chr5:179289400-179292200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr5:179289400-179292200	Strong transcription	Psoas Muscle	Psoas

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