Variant report

Variant	rs3813523
Chromosome Location	chr9:104249448-104249449
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	chr9:104249195-104249659	A549	lung:	n/a	n/a
2	MAX	chr9:104249126-104249743	ECC-1	luminal epithelium:	n/a	chr9:104249383-104249393
3	CTCF	chr9:104248835-104249830	A549	lung:	n/a	chr9:104248961-104248974
4	CTCF	chr9:104249440-104249590	BJ	skin:	n/a	n/a
5	TCF7L2	chr9:104249370-104249715	PANC-1	pancreas:	n/a	n/a
6	RAD21	chr9:104249383-104249687	A549	lung:	n/a	n/a
7	CTCF	chr9:104249413-104249604	Kidney_OC	kidney:	n/a	n/a
8	USF1	chr9:104249042-104249902	HCT-116	colon:	n/a	n/a
9	RAD21	chr9:104249239-104249719	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:104248082-104250359	PBDE	blood:	n/a	n/a
11	CTCF	chr9:104249420-104249570	HMF	breast:	n/a	n/a
12	POLR2A	chr9:104249131-104249720	PANC-1	pancreas:	n/a	n/a
13	CTCF	chr9:104249440-104249590	HMEC	breast:	n/a	n/a
14	POLR2A	chr9:104248198-104249575	Hela-S3	cervix:	n/a	n/a
15	MYC	chr9:104249206-104249656	K562	blood:	n/a	chr9:104249383-104249393
16	CTCF	chr9:104249420-104249570	HA-sp	spinal cord:	n/a	n/a
17	REST	chr9:104248182-104249912	H1-neurons	neurons:	n/a	chr9:104248312-104248332 chr9:104248897-104248910 chr9:104249017-104249030 chr9:104248886-104248904 chr9:104248498-104248518
18	POLR2A	chr9:104249190-104249630	U87	brain:	n/a	n/a
19	MAX	chr9:104248139-104249702	H1-hESC	embryonic stem cell:	n/a	chr9:104249383-104249393
20	CTCF	chr9:104249400-104249550	WERI-Rb-1	eye:	n/a	n/a
21	CHD2	chr9:104248249-104249772	H1-hESC	embryonic stem cell:	n/a	chr9:104249495-104249502 chr9:104249381-104249391
22	TBP	chr9:104249269-104249637	K562	blood:	n/a	n/a
23	MAX	chr9:104249090-104249650	ECC-1	luminal epithelium:	n/a	chr9:104249383-104249393
24	POLR2A	chr9:104248993-104249623	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr9:104248069-104249787	H1-hESC	embryonic stem cell:	n/a	chr9:104249383-104249393
26	YY1	chr9:104249202-104249556	K562	blood:	n/a	chr9:104249316-104249338
27	CTCF	chr9:104249440-104249590	HRPEpiC	eye:	n/a	n/a
28	MAX	chr9:104248003-104250096	A549	lung:	n/a	chr9:104249383-104249393
29	TCF7L2	chr9:104248845-104249622	Hela-S3	cervix:	n/a	n/a
30	TAF1	chr9:104249281-104249535	K562	blood:	n/a	n/a
31	CTCF	chr9:104249400-104249550	HCT-116	colon:	n/a	n/a
32	POLR2A	chr9:104248143-104249813	HCT-116	colon:	n/a	n/a
33	USF1	chr9:104249282-104249560	SK-N-SH_RA	brain:	n/a	n/a
34	CREB1	chr9:104249057-104249589	A549	lung:	n/a	n/a
35	RAD21	chr9:104249205-104249674	IMR90	lung:	n/a	n/a
36	FOXA2	chr9:104249363-104249836	A549	lung:	n/a	n/a
37	SMC3	chr9:104249275-104249684	Hela-S3	cervix:	n/a	n/a
38	USF1	chr9:104249223-104249586	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr9:104249380-104249530	HCFaa	heart:	n/a	n/a
40	POLR2A	chr9:104248254-104249621	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr9:104249420-104249570	HEK293	kidney:	n/a	n/a
42	MAX	chr9:104249255-104249865	A549	lung:	n/a	chr9:104249383-104249393
43	POLR2A	chr9:104248204-104249724	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr9:104249230-104249645	A549	lung:	n/a	n/a
45	MAX	chr9:104249276-104250000	H1-hESC	embryonic stem cell:	n/a	chr9:104249383-104249393
46	USF1	chr9:104249248-104249557	K562	blood:	n/a	n/a
47	CTCF	chr9:104249420-104249570	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr9:104249230-104249623	Hela-S3	cervix:	n/a	n/a
49	E2F6	chr9:104249261-104249503	K562	blood:	n/a	chr9:104249495-104249502 chr9:104249381-104249392
50	REST	chr9:104249166-104249705	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104159029..104163428-chr9:104247830..104250587,4	K562	blood:

Variant related genes	Relation type
TMEM246	TF binding region
ENSG00000136897	Chromatin interaction
ENSG00000136870	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11793946	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16920437	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16920477	0.81[ASN][1000 genomes]
rs16920487	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1929483	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2417271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28411396	0.81[ASN][1000 genomes]
rs56998622	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575836	0.81[ASN][1000 genomes]
rs62575837	0.81[ASN][1000 genomes]
rs72745305	0.81[ASN][1000 genomes]
rs7872953	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs989900	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs989901	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104247600-104249600	Active TSS	K562	blood
2	chr9:104247600-104250000	Active TSS	Brain Angular Gyrus	brain
3	chr9:104247600-104250200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:104247800-104249600	Active TSS	Colon Smooth Muscle	Colon
5	chr9:104247800-104249600	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr9:104247800-104249800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr9:104247800-104249800	Active TSS	Right Atrium	heart
8	chr9:104247800-104250000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:104247800-104250000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr9:104248000-104249600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:104248000-104249600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr9:104248000-104249600	Active TSS	Fetal Intestine Large	intestine
13	chr9:104248000-104249600	Active TSS	Fetal Intestine Small	intestine
14	chr9:104248000-104249600	Active TSS	Hela-S3	cervix
15	chr9:104248000-104249800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr9:104248000-104249800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:104248000-104249800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:104248000-104249800	Active TSS	Brain Anterior Caudate	brain
19	chr9:104248000-104249800	Active TSS	Brain Cingulate Gyrus	brain
20	chr9:104248000-104249800	Active TSS	Duodenum Mucosa	Duodenum
21	chr9:104248000-104249800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:104248000-104249800	Active TSS	Ovary	ovary
23	chr9:104248000-104250000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:104248000-104250000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:104248000-104250000	Active TSS	Rectal Smooth Muscle	rectum
26	chr9:104248000-104250000	Active TSS	Stomach Mucosa	stomach
27	chr9:104248200-104249600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:104248200-104249600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr9:104248200-104249600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:104248200-104249600	Active TSS	Gastric	stomach
31	chr9:104248200-104249600	Active TSS	Left Ventricle	heart
32	chr9:104248200-104249600	Active TSS	A549	lung
33	chr9:104248200-104249800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr9:104248200-104249800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:104248200-104249800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:104248200-104249800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:104248200-104249800	Active TSS	Aorta	Aorta
38	chr9:104248200-104249800	Active TSS	Brain Substantia Nigra	brain
39	chr9:104248200-104249800	Active TSS	Fetal Kidney	kidney
40	chr9:104248200-104249800	Active TSS	Psoas Muscle	Psoas
41	chr9:104248200-104249800	Active TSS	HSMMtube	muscle
42	chr9:104248200-104249800	Active TSS	NHDF-Ad	bronchial
43	chr9:104248200-104250000	Active TSS	Pancreas	Pancrea
44	chr9:104248200-104250000	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr9:104248400-104249600	Active TSS	Fetal Heart	heart
46	chr9:104248400-104249800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr9:104248400-104250000	Active TSS	Fetal Brain Male	brain
48	chr9:104248600-104249600	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr9:104248600-104249600	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr9:104248600-104249600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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