Variant report

Variant	rs3809139
Chromosome Location	chr12:26279568-26279569
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	USF1	chr12:26279143-26279907	SK-N-SH	brain:	n/a	chr12:26279655-26279671 chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
2	MAX	chr12:26278476-26279791	MCF-7	breast:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
3	HA-E2F1	chr12:26278327-26279859	MCF-7	breast:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26278868-26278877 chr12:26279656-26279666 chr12:26279058-26279068
4	CTCF	chr12:26279540-26279690	HBMEC	blood vessel:	n/a	n/a
5	EP300	chr12:26279369-26279693	SK-N-SH_RA	brain:	n/a	chr12:26279660-26279669 chr12:26279574-26279590 chr12:26279508-26279524 chr12:26279657-26279666 chr12:26279581-26279590
6	POLR2A	chr12:26279512-26279641	ProgFib	skin:	n/a	n/a
7	MAX	chr12:26278916-26279681	A549	lung:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
8	MAX	chr12:26279393-26279763	H1-hESC	embryonic stem cell:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
9	MAX	chr12:26278459-26279869	SK-N-SH	brain:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
10	USF1	chr12:26278974-26279707	A549	lung:	n/a	chr12:26279048-26279064 chr12:26279655-26279671 chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
11	CREB1	chr12:26279360-26279746	A549	lung:	n/a	n/a
12	CTCF	chr12:26279540-26279690	GM12873	blood:	n/a	n/a
13	E2F6	chr12:26279409-26279824	A549	lung:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26279656-26279666
14	MYC	chr12:26277620-26279870	NB4	blood:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
15	CTCF	chr12:26279557-26279791	IMR90	lung:	n/a	n/a
16	RAD21	chr12:26278816-26279837	IMR90	lung:	n/a	chr12:26279414-26279427 chr12:26279416-26279426 chr12:26279001-26279015
17	FOSL2	chr12:26278696-26279810	SK-N-SH	brain:	n/a	chr12:26278869-26278878 chr12:26279134-26279144 chr12:26279135-26279144 chr12:26278870-26278879 chr12:26279135-26279142 chr12:26279134-26279145
18	SMC3	chr12:26278373-26279819	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr12:26279372-26279767	ECC-1	luminal epithelium:	n/a	n/a
20	MAZ	chr12:26279321-26279683	GM12878	blood:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
21	E2F6	chr12:26278326-26279896	A549	lung:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26278868-26278877 chr12:26279656-26279666 chr12:26279058-26279068
22	FOXA2	chr12:26278872-26279688	A549	lung:	n/a	n/a
23	REST	chr12:26278573-26280033	H1-neurons	neurons:	n/a	chr12:26279049-26279062 chr12:26279049-26279062
24	CTCF	chr12:26279560-26279710	GM12870	blood:	n/a	n/a
25	SIN3AK20	chr12:26279335-26279744	SK-N-SH	brain:	n/a	n/a
26	USF1	chr12:26278811-26279855	ECC-1	luminal epithelium:	n/a	chr12:26279048-26279064 chr12:26279655-26279671 chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
27	RAD21	chr12:26279542-26279753	A549	lung:	n/a	n/a
28	POLR2A	chr12:26279505-26279583	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF1	chr12:26279353-26279648	GM12878	blood:	n/a	chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
30	TAF1	chr12:26278776-26279770	SK-N-SH	brain:	n/a	n/a
31	E2F6	chr12:26279416-26279671	K562	blood:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26279656-26279666
32	SPI1	chr12:26279509-26279848	HL-60	blood:	n/a	n/a
33	MAX	chr12:26277378-26279826	NB4	blood:	n/a	chr12:26279525-26279534 chr12:26277873-26277883 chr12:26278212-26278222 chr12:26279524-26279535 chr12:26278316-26278324 chr12:26279525-26279534
34	RAD21	chr12:26279419-26279823	SK-N-SH_RA	brain:	n/a	n/a
35	JUND	chr12:26278960-26279813	H1-hESC	embryonic stem cell:	n/a	chr12:26279134-26279144 chr12:26279135-26279144 chr12:26279135-26279142 chr12:26279133-26279144 chr12:26279134-26279145
36	GATA2	chr12:26278829-26279568	HUVEC	blood vessel:	n/a	n/a
37	USF1	chr12:26278913-26279899	HCT-116	colon:	n/a	chr12:26279048-26279064 chr12:26279655-26279671 chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
38	POLR2A	chr12:26278456-26279820	SK-N-SH	brain:	n/a	n/a
39	HA-E2F1	chr12:26278683-26279714	Hela-S3	cervix:	n/a	chr12:26279497-26279509 chr12:26279508-26279518 chr12:26279659-26279669 chr12:26278868-26278877 chr12:26279656-26279666 chr12:26279058-26279068
40	POLR2A	chr12:26277806-26279712	HEK293	kidney:	n/a	n/a
41	EP300	chr12:26279366-26279670	SK-N-SH_RA	brain:	n/a	chr12:26279660-26279669 chr12:26279574-26279590 chr12:26279508-26279524 chr12:26279657-26279666 chr12:26279581-26279590
42	UBTF	chr12:26279467-26279667	K562	blood:	n/a	n/a
43	USF1	chr12:26279031-26279780	SK-N-SH_RA	brain:	n/a	chr12:26279048-26279064 chr12:26279655-26279671 chr12:26279578-26279594 chr12:26279588-26279604 chr12:26279563-26279579 chr12:26279576-26279592
44	JUND	chr12:26277150-26280021	SK-N-SH	brain:	n/a	chr12:26277187-26277196 chr12:26278869-26278878 chr12:26279134-26279144 chr12:26279135-26279144 chr12:26278870-26278879 chr12:26278366-26278375 chr12:26279135-26279142 chr12:26277193-26277202 chr12:26277188-26277197 chr12:26277192-26277201 chr12:26279133-26279144 chr12:26279134-26279145
45	ZNF263	chr12:26278292-26279795	HEK293-T-REx	kidney:	n/a	chr12:26279548-26279557 chr12:26279516-26279525
46	MAX	chr12:26279300-26279815	H1-hESC	embryonic stem cell:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
47	SIN3A	chr12:26277737-26279739	H1-hESC	embryonic stem cell:	n/a	chr12:26279511-26279522 chr12:26279605-26279619
48	CCNT2	chr12:26279331-26279674	K562	blood:	n/a	n/a
49	MAX	chr12:26279379-26279763	K562	blood:	n/a	chr12:26279525-26279534 chr12:26279524-26279535 chr12:26279525-26279534
50	POLR2A	chr12:26279462-26279736	HCT-116	colon:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:26279544-26279594	T-47D	breast:	n/a
2	chr12:26279544-26279594	ProgFib	skin:	n/a
3	chr12:26279544-26279594	GM12891	blood:	n/a
4	chr12:26279544-26279594	SAEC	small airway:	n/a
5	chr12:26279544-26279594	Hepatocyte	liver:	n/a
6	chr12:26279544-26279594	GM19239	blood:	n/a
7	chr12:26279544-26279594	AG04450	lung:	fetal
8	chr12:26279544-26279594	HCPEpiC	choroid plexus:	n/a
9	chr12:26279544-26279594	HEEpiC	esophagus:	n/a
10	chr12:26279544-26279594	AG09319	gingival:	n/a
11	chr12:26279544-26279594	HRE	kidney:	n/a
12	chr12:26279544-26279594	HNPCEpiC	eye:	n/a
13	chr12:26279544-26279594	HRCEpiC	kidney:	n/a
14	chr12:26279544-26279594	AG09309	skin:	n/a
15	chr12:26279544-26279594	HepG2	liver:	n/a
16	chr12:26279544-26279594	MCF10A-Er-Src	breast:	n/a
17	chr12:26279544-26279594	BE2_C	brain:	n/a
18	chr12:26279544-26279594	RPTEC	kidney:	n/a
19	chr12:26279544-26279594	NB4	blood:	n/a
20	chr12:26279544-26279594	NHDF-neo	bronchial:	n/a
21	chr12:26279544-26279594	SK-N-SH	brain:	n/a
22	chr12:26279544-26279594	GM12878	blood:	n/a
23	chr12:26279544-26279594	HEK293	kidney:	embryo
24	chr12:26279544-26279594	HCT-116	colon:	n/a
25	chr12:26279544-26279594	AG10803	skin:	n/a
26	chr12:26279544-26279594	ECC-1	luminal epithelium:	n/a
27	chr12:26279544-26279594	SKMC	muscle:	n/a
28	chr12:26279544-26279594	Jurkat	blood:	n/a
29	chr12:26279544-26279594	HCF	heart:	n/a
30	chr12:26279544-26279594	CMK	blood:	n/a
31	chr12:26279544-26279594	HL-60	blood:	n/a
32	chr12:26279544-26279594	SK-N-SH_RA	brain:	n/a
33	chr12:26279544-26279594	A549	lung:	n/a
34	chr12:26279544-26279594	NT2-D1	testis:	n/a
35	chr12:26279544-26279594	PrEC	prostate:	n/a
36	chr12:26279544-26279594	HIPEpiC	eye:	n/a
37	chr12:26279544-26279594	LNCaP	prostate:	n/a
38	chr12:26279544-26279594	HPAEpiC	pulmonary alveolar:	n/a
39	chr12:26279544-26279594	PANC-1	pancreas:	n/a
40	chr12:26279544-26279594	Hela-S3	cervix:	n/a
41	chr12:26279544-26279594	HMEC	breast:	n/a
42	chr12:26279544-26279594	H1-hESC	embryonic stem cell:	embryo
43	chr12:26279544-26279594	AG04449	skin:	fetal
44	chr12:26279544-26279594	GM06990	blood:	n/a
45	chr12:26279544-26279594	BJ	skin:	n/a
46	chr12:26279544-26279594	NHBE	bronchial:	n/a
47	chr12:26279544-26279594	GM12892	blood:	n/a
48	chr12:26279544-26279594	AoSMC	blood vessel:	n/a
49	chr12:26279544-26279594	K562	blood:	n/a
50	chr12:26279544-26279594	HCM	heart:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26275273..26277209-chr12:26278660..26280315,2	K562	blood:
2	chr12:26274388..26277209-chr12:26277264..26280315,5	K562	blood:

Variant related genes	Relation type
ENSG00000256894	TF binding region
BHLHE41	TF binding region
BHLHE41	CpG island
ENSG00000256894	CpG island
ENSG00000123096	Chromatin interaction
ENSG00000123095	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10431216	0.81[ASN][1000 genomes]
rs1466467	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55678992	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61915713	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61915714	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61915715	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61915716	1.00[ASN][1000 genomes]
rs61915717	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898932	chr12:26262137-26283482	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv898933	chr12:26262137-26285006	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26272200-26280000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:26273000-26280000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr12:26273400-26280000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr12:26273400-26280000	Active TSS	Right Atrium	heart
5	chr12:26273600-26279800	Active TSS	Psoas Muscle	Psoas
6	chr12:26273600-26280000	Active TSS	Brain Substantia Nigra	brain
7	chr12:26274000-26280000	Active TSS	Brain Angular Gyrus	brain
8	chr12:26274200-26279600	Active TSS	Colon Smooth Muscle	Colon
9	chr12:26274400-26279800	Active TSS	NHDF-Ad	bronchial
10	chr12:26274400-26280200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:26274600-26280000	Active TSS	Aorta	Aorta
12	chr12:26274600-26280000	Active TSS	Right Ventricle	heart
13	chr12:26274600-26280000	Active TSS	HSMM	muscle
14	chr12:26274800-26279800	Active TSS	Left Ventricle	heart
15	chr12:26274800-26280000	Active TSS	Ovary	ovary
16	chr12:26275000-26279800	Active TSS	Brain Anterior Caudate	brain
17	chr12:26275000-26279800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
18	chr12:26275000-26280000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:26275000-26280000	Active TSS	Brain Cingulate Gyrus	brain
20	chr12:26275000-26280400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:26276600-26279800	Active TSS	Brain Hippocampus Middle	brain
22	chr12:26276600-26279800	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:26276800-26279600	Active TSS	HMEC	breast
24	chr12:26276800-26279800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:26276800-26279800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:26276800-26279800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
27	chr12:26276800-26280000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr12:26277000-26279800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:26277000-26279800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr12:26277400-26279600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
31	chr12:26277400-26279800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:26277400-26279800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr12:26277600-26279600	Active TSS	Esophagus	oesophagus
34	chr12:26277600-26279600	Active TSS	Placenta Amnion	Placenta Amnion
35	chr12:26277600-26279800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:26277800-26279600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr12:26277800-26279600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:26277800-26279600	Enhancers	Spleen	Spleen
39	chr12:26277800-26279800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr12:26277800-26279800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:26277800-26279800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr12:26277800-26279800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr12:26277800-26279800	Active TSS	Primary B cells from peripheral blood	blood
44	chr12:26277800-26279800	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr12:26277800-26279800	Active TSS	Osteobl	bone
46	chr12:26277800-26280000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:26277800-26280000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr12:26277800-26280000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr12:26277800-26280400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
50	chr12:26278000-26279600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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