Variant report

Variant	rs655497
Chromosome Location	chr9:22446828-22446829
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	POLR2A	chr9:22446620-22447666	MCF-7	breast:	n/a	n/a
2	MAX	chr9:22446278-22448068	A549	lung:	n/a	n/a
3	POLR2A	chr9:22446735-22447006	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr9:22446469-22447698	Hela-S3	cervix:	n/a	n/a
5	CHD1	chr9:22446807-22447400	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr9:22446333-22446842	H1-hESC	embryonic stem cell:	n/a	chr9:22446688-22446697
7	SMARCB1	chr9:22446783-22447750	Hela-S3	cervix:	n/a	n/a
8	BACH1	chr9:22446601-22447549	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr9:22446558-22447694	MCF-7	breast:	n/a	n/a
10	TCF7L2	chr9:22446630-22447773	Hela-S3	cervix:	n/a	n/a
11	E2F4	chr9:22446606-22446916	MCF10A-Er-Src	breast:	n/a	chr9:22446688-22446697
12	JUND	chr9:22446817-22446884	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr9:22446613-22448844	A549	lung:	n/a	n/a
14	RAD21	chr9:22446638-22447690	H1-hESC	embryonic stem cell:	n/a	chr9:22446691-22446703
15	POLR2A	chr9:22446765-22447021	Gliobla	brain:	n/a	n/a
16	ELF1	chr9:22446400-22447162	MCF-7	breast:	n/a	chr9:22446750-22446762
17	MAX	chr9:22446318-22447023	ECC-1	luminal epithelium:	n/a	n/a
18	TBP	chr9:22446667-22447648	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr9:22446717-22447043	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF143	chr9:22446816-22447601	Hela-S3	cervix:	n/a	chr9:22446977-22446987
21	POLR2A	chr9:22446590-22447785	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr9:22446733-22446940	A549	lung:	n/a	n/a
23	SIN3A	chr9:22446758-22447497	H1-hESC	embryonic stem cell:	n/a	chr9:22446881-22446890
24	POLR2A	chr9:22446583-22447633	HUVEC	blood vessel:	n/a	n/a
25	MAX	chr9:22446430-22446860	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr9:22446577-22448100	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr9:22446412-22447134	A549	lung:	n/a	n/a
28	ELF1	chr9:22446587-22447284	MCF-7	breast:	n/a	chr9:22446750-22446762
29	ZNF143	chr9:22446727-22446913	H1-hESC	embryonic stem cell:	n/a	n/a
30	TAF1	chr9:22446618-22447982	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr9:22446658-22447010	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr9:22446669-22447561	Hela-S3	cervix:	n/a	n/a
33	E2F6	chr9:22446232-22446981	A549	lung:	n/a	chr9:22446688-22446697
34	MAZ	chr9:22446536-22447952	Hela-S3	cervix:	n/a	n/a
35	SMC3	chr9:22446752-22447667	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr9:22446696-22447105	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr9:22446737-22447702	A549	lung:	n/a	n/a
38	PML	chr9:22446719-22447030	MCF-7	breast:	n/a	n/a
39	HDAC2	chr9:22446552-22447458	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr9:22446720-22447025	ECC-1	luminal epithelium:	n/a	n/a
41	RAD21	chr9:22446794-22447613	H1-hESC	embryonic stem cell:	n/a	n/a
42	CHD2	chr9:22446579-22447049	Hela-S3	cervix:	n/a	chr9:22446718-22446728
43	RFX5	chr9:22446445-22447609	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr9:22446786-22446917	A549	lung:	n/a	n/a
45	CTBP2	chr9:22446617-22448118	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr9:22446735-22446991	H1-hESC	embryonic stem cell:	n/a	n/a
47	TAF1	chr9:22446655-22447123	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr9:22446767-22447069	ProgFib	skin:	n/a	n/a
49	ZNF263	chr9:22446638-22448412	HEK293-T-REx	kidney:	n/a	chr9:22446654-22446663 chr9:22446697-22446706
50	E2F6	chr9:22446488-22446863	A549	lung:	n/a	chr9:22446688-22446697

Variant related genes	Relation type
DMRTA1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1329399	0.93[ASN][1000 genomes]
rs2247403	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247404	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506311	0.86[ASN][1000 genomes]
rs533644	0.87[ASN][1000 genomes]
rs535470	0.87[ASN][1000 genomes]
rs558612	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs560612	0.80[AFR][1000 genomes]
rs563802	0.88[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs665908	0.86[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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1031822	chr9:22364573-22490686	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv892750	chr9:22383816-22496640	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1016983	chr9:22412948-22672062	Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1027227	chr9:22416348-22666768	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv540088	chr9:22416348-22666768	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs655497	ADAMTSL1	cis	cerebellum	SCAN
rs655497	KLHL9	cis	cerebellum	SCAN
rs655497	IFNW1	cis	cerebellum	SCAN
rs655497	DMRTA1	cis	Skin Sun Exposed Lower leg	GTEx
rs655497	DMRTA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22446000-22450400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:22446200-22447000	Active TSS	Stomach Smooth Muscle	stomach
3	chr9:22446200-22447600	Active TSS	NH-A	brain
4	chr9:22446200-22447800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr9:22446200-22447800	Active TSS	Aorta	Aorta
6	chr9:22446200-22447800	Active TSS	Colon Smooth Muscle	Colon
7	chr9:22446200-22449000	Active TSS	Brain Anterior Caudate	brain
8	chr9:22446200-22449200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr9:22446200-22449600	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr9:22446200-22450000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr9:22446400-22447000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:22446400-22447000	Active TSS	Left Ventricle	heart
13	chr9:22446400-22447200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:22446400-22447200	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr9:22446400-22447200	Active TSS	Colonic Mucosa	Colon
16	chr9:22446400-22447400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
17	chr9:22446400-22447600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr9:22446400-22447600	Active TSS	HSMMtube	muscle
19	chr9:22446400-22447600	Active TSS	NHLF	lung
20	chr9:22446400-22447800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:22446400-22448000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr9:22446400-22448000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:22446400-22448000	Active TSS	Brain Angular Gyrus	brain
24	chr9:22446400-22448000	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr9:22446400-22448000	Active TSS	Brain Substantia Nigra	brain
26	chr9:22446400-22448000	Active TSS	Psoas Muscle	Psoas
27	chr9:22446400-22448000	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:22446400-22448000	Active TSS	HMEC	breast
29	chr9:22446400-22448200	Active TSS	Pancreas	Pancrea
30	chr9:22446400-22448200	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr9:22446400-22448200	Active TSS	Right Atrium	heart
32	chr9:22446400-22448200	Active TSS	NHEK	skin
33	chr9:22446400-22448400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:22446400-22448400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:22446400-22448400	Active TSS	Gastric	stomach
36	chr9:22446400-22449000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:22446400-22449000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:22446400-22449200	Active TSS	H9 Cell Line	embryonic stem cell
39	chr9:22446400-22449200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:22446400-22449200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:22446400-22449400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr9:22446600-22447000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr9:22446600-22447000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr9:22446600-22447000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:22446600-22447000	Bivalent Enhancer	Fetal Brain Male	brain
46	chr9:22446600-22447200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:22446600-22447200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:22446600-22447200	Active TSS	Adipose Nuclei	Adipose
49	chr9:22446600-22447400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:22446600-22447400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood

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