Variant report

Variant	rs9609157
Chromosome Location	chr22:31318341-31318342
allele	C/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	PAX5	chr22:31318095-31318380	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:31318263-31318357	HepG2	liver:	n/a	n/a
3	POLR2A	chr22:31318094-31318410	ECC-1	luminal epithelium:	n/a	n/a
4	FOXM1	chr22:31318195-31318584	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:31317902-31318671	GM18505	blood:	n/a	n/a
6	MAX	chr22:31318094-31318635	GM12878	blood:	n/a	n/a
7	BHLHE40	chr22:31317649-31318716	GM12878	blood:	n/a	chr22:31318278-31318287 chr22:31318278-31318287 chr22:31318272-31318293 chr22:31318277-31318286
8	USF1	chr22:31318156-31318409	GM12878	blood:	n/a	chr22:31318278-31318287 chr22:31318278-31318287 chr22:31318272-31318293 chr22:31318277-31318286
9	EBF1	chr22:31318096-31318371	GM12878	blood:	n/a	n/a
10	ZBTB33	chr22:31317994-31318489	GM12878	blood:	n/a	n/a
11	NRF1	chr22:31317489-31318575	SK-N-SH	brain:	n/a	chr22:31318251-31318265 chr22:31318254-31318263 chr22:31318256-31318265 chr22:31318254-31318268 chr22:31318254-31318265
12	ZBTB33	chr22:31318076-31318451	GM12878	blood:	n/a	n/a
13	POLR2A	chr22:31317908-31318841	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr22:31318059-31318667	GM12878	blood:	n/a	n/a
15	USF1	chr22:31318092-31318426	GM12878	blood:	n/a	chr22:31318278-31318287 chr22:31318278-31318287 chr22:31318272-31318293 chr22:31318277-31318286
16	PAX5	chr22:31317878-31318571	GM12878	blood:	n/a	n/a
17	MYC	chr22:31318219-31318422	HUVEC	blood vessel:	n/a	n/a
18	POU2F2	chr22:31318163-31318398	GM12878	blood:	n/a	n/a
19	NRF1	chr22:31318051-31318478	GM12878	blood:	n/a	chr22:31318251-31318265 chr22:31318254-31318263 chr22:31318256-31318265 chr22:31318254-31318268 chr22:31318254-31318265
20	POLR2A	chr22:31317898-31318861	MCF-7	breast:	n/a	n/a
21	POLR2A	chr22:31317930-31318673	GM12878	blood:	n/a	n/a
22	POLR2A	chr22:31318094-31318526	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr22:31318074-31318626	H1-hESC	embryonic stem cell:	n/a	n/a
24	ELF1	chr22:31318069-31318664	GM12878	blood:	n/a	chr22:31318538-31318550
25	RUNX3	chr22:31318029-31318547	GM12878	blood:	n/a	n/a
26	POU2F2	chr22:31318033-31318613	GM12878	blood:	n/a	n/a
27	POLR2A	chr22:31318000-31318659	GM12878	blood:	n/a	n/a
28	SPI1	chr22:31318253-31318426	GM12878	blood:	n/a	n/a
29	POLR2A	chr22:31318171-31318761	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr22:31317616-31318734	GM12891	blood:	n/a	n/a
31	POLR2A	chr22:31318075-31318598	GM12892	blood:	n/a	n/a
32	POLR2A	chr22:31317994-31318584	GM15510	blood:	n/a	n/a
33	ELF1	chr22:31317903-31318690	GM12878	blood:	n/a	chr22:31318538-31318550
34	MAX	chr22:31318093-31318470	HUVEC	blood vessel:	n/a	n/a
35	PAX5	chr22:31317852-31318623	GM12878	blood:	n/a	n/a
36	POLR2A	chr22:31317887-31318741	GM12878	blood:	n/a	n/a
37	POLR2A	chr22:31318185-31318548	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr22:31318052-31318516	GM18951	blood:	n/a	n/a
39	MYC	chr22:31318219-31318343	GM12878	blood:	n/a	n/a
40	POU2F2	chr22:31318173-31318546	GM12878	blood:	n/a	n/a
41	POLR2A	chr22:31318070-31318688	HUVEC	blood vessel:	n/a	n/a
42	PML	chr22:31317871-31318600	GM12878	blood:	n/a	n/a
43	POLR2A	chr22:31318009-31318607	GM19193	blood:	n/a	n/a
44	NFIC	chr22:31318064-31318551	GM12878	blood:	n/a	n/a
45	POLR2A	chr22:31318026-31318511	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr22:31318087-31318405	GM12891	blood:	n/a	n/a
47	POLR2A	chr22:31318083-31318658	GM12878	blood:	n/a	n/a
48	ZNF143	chr22:31318150-31318436	GM12878	blood:	n/a	n/a
49	POLR2A	chr22:31318099-31318652	GM12878	blood:	n/a	n/a
50	HA-E2F1	chr22:31317811-31318514	MCF-7	breast:	n/a	chr22:31318255-31318264

No.	Distal block	Cell Line	Cell type
1	chr22:31158219..31160716-chr22:31317751..31319382,2	K562	blood:
2	chr22:31158390..31161654-chr22:31315788..31318935,3	MCF-7	breast:
3	chr22:31218130..31220095-chr22:31317473..31320044,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OSBP2-1	chr22:31318332-31318502	ENSG00000235989.2
2	lnc-OSBP2-1	chr22:31318316-31318502	NONHSAT084818
3	lnc-OSBP2-1	chr22:31318332-31318502	ENSG00000235989.3

Variant related genes	Relation type
MORC2-AS1	TF binding region
ENSG00000184792	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2107402	0.82[EUR][1000 genomes]
rs9606794	0.81[ASN][1000 genomes]
rs9606799	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9609154	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609160	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9609163	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9609168	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9609189	0.84[EUR][1000 genomes]
rs9609192	0.82[EUR][1000 genomes]

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	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9609157	TUG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31278600-31321400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:31283600-31318400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:31290800-31320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr22:31295400-31321000	Weak transcription	HSMMtube	muscle
5	chr22:31300200-31320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:31304200-31320800	Weak transcription	Gastric	stomach
7	chr22:31304600-31320400	Weak transcription	Lung	lung
8	chr22:31305600-31319200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr22:31305600-31320200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr22:31306000-31319600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr22:31306800-31320200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr22:31306800-31320200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr22:31311400-31319800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr22:31312000-31320000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr22:31312200-31320000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr22:31313000-31319800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr22:31316200-31320600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr22:31316600-31318400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr22:31316600-31318600	Active TSS	Brain Anterior Caudate	brain
20	chr22:31316600-31318800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr22:31316800-31323000	Weak transcription	Hela-S3	cervix
22	chr22:31317000-31318400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr22:31317000-31319800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:31317200-31318400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:31317200-31318600	Active TSS	Brain Angular Gyrus	brain
26	chr22:31317200-31318600	Active TSS	Rectal Smooth Muscle	rectum
27	chr22:31317400-31318400	Active TSS	Fetal Intestine Large	intestine
28	chr22:31317400-31318400	Active TSS	Psoas Muscle	Psoas
29	chr22:31317400-31318600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr22:31317400-31318600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:31317400-31318600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr22:31317400-31318600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr22:31317400-31318600	Active TSS	Brain Hippocampus Middle	brain
34	chr22:31317400-31318600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr22:31317400-31318600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:31317400-31318600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr22:31317400-31318600	Flanking Active TSS	HUVEC	blood vessel
38	chr22:31317400-31318600	Active TSS	NHLF	lung
39	chr22:31317400-31318800	Active TSS	Primary T cells from cord blood	blood
40	chr22:31317400-31318800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr22:31317400-31318800	Active TSS	Thymus	Thymus
42	chr22:31317600-31318400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:31317600-31318400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr22:31317600-31318400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr22:31317600-31318400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr22:31317600-31318400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr22:31317600-31318400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr22:31317600-31318400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
49	chr22:31317600-31318400	Active TSS	Left Ventricle	heart
50	chr22:31317600-31318400	Active TSS	Skeletal Muscle Female	skeletal muscle

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