Variant report

Variant	rs3809191
Chromosome Location	chr12:117176381-117176382
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	MTA3	chr12:117175862-117176592	GM12878	blood:	n/a	n/a
2	CTCF	chr12:117176360-117176510	GM12873	blood:	n/a	n/a
3	CREB1	chr12:117175684-117176491	H1-hESC	embryonic stem cell:	n/a	n/a
4	RELA	chr12:117175435-117176458	GM18951	blood:	n/a	n/a
5	SP1	chr12:117175367-117176612	HCT-116	colon:	n/a	chr12:117175884-117175896 chr12:117176063-117176084 chr12:117175953-117175974 chr12:117175886-117175895 chr12:117175873-117175882 chr12:117175985-117175996 chr12:117175885-117175894 chr12:117175884-117175896
6	POLR2A	chr12:117175415-117176619	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr12:117176340-117176490	WERI-Rb-1	eye:	n/a	n/a
8	MAX	chr12:117175593-117176605	SK-N-SH	brain:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
9	RELA	chr12:117175636-117176599	GM10847	blood:	n/a	n/a
10	FOXM1	chr12:117175737-117176584	GM12878	blood:	n/a	n/a
11	ELF1	chr12:117175681-117176442	MCF-7	breast:	n/a	chr12:117175885-117175897
12	MAX	chr12:117175592-117176543	ECC-1	luminal epithelium:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
13	TAF1	chr12:117175586-117176401	ECC-1	luminal epithelium:	n/a	n/a
14	SMC3	chr12:117175538-117176605	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr12:117176300-117176450	Hela-S3	cervix:	n/a	n/a
16	E2F6	chr12:117175492-117176463	K562	blood:	n/a	chr12:117175886-117175895
17	SIX5	chr12:117175850-117176401	A549	lung:	n/a	n/a
18	ELF1	chr12:117175352-117176384	MCF-7	breast:	n/a	chr12:117175885-117175897
19	CTCF	chr12:117176300-117176450	GM12868	blood:	n/a	n/a
20	MAX	chr12:117175468-117176638	MCF-7	breast:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
21	RCOR1	chr12:117175757-117176573	Hela-S3	cervix:	n/a	n/a
22	MAX	chr12:117175670-117176484	MCF-7	breast:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
23	SIN3AK20	chr12:117175463-117176533	SK-N-SH	brain:	n/a	n/a
24	CTCF	chr12:117176300-117176450	GM12867	blood:	n/a	n/a
25	GATA2	chr12:117175875-117176387	SH-SY5Y	brain:	n/a	chr12:117176124-117176132
26	GABPA	chr12:117175544-117176638	MCF-7	breast:	n/a	n/a
27	POLR2A	chr12:117175307-117176591	Raji	blood:	n/a	n/a
28	BRCA1	chr12:117175902-117176487	GM12878	blood:	n/a	n/a
29	MAX	chr12:117175392-117176495	Hela-S3	cervix:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
30	RUNX3	chr12:117175624-117176392	GM12878	blood:	n/a	n/a
31	STAT5A	chr12:117175737-117176590	GM12878	blood:	n/a	chr12:117175980-117175992
32	POLR2A	chr12:117175590-117176437	HEK293	kidney:	n/a	n/a
33	CTCF	chr12:117176280-117176430	GM12872	blood:	n/a	n/a
34	CTCF	chr12:117176320-117176470	HRE	kidney:	n/a	n/a
35	ZNF263	chr12:117174095-117176469	HEK293-T-REx	kidney:	n/a	chr12:117175450-117175471 chr12:117175567-117175576 chr12:117175385-117175406 chr12:117175429-117175450
36	ZEB1	chr12:117175819-117176499	GM12878	blood:	n/a	n/a
37	MXI1	chr12:117175449-117176658	GM12878	blood:	n/a	chr12:117175866-117175875
38	TCF7L2	chr12:117175868-117176619	Hela-S3	cervix:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
39	JUN	chr12:117175008-117176480	K562	blood:	n/a	n/a
40	FOSL1	chr12:117175606-117176405	HCT-116	colon:	n/a	n/a
41	CTCF	chr12:117176354-117176388	GM12878	blood:	n/a	n/a
42	CTCF	chr12:117176240-117176390	GM12871	blood:	n/a	n/a
43	MAX	chr12:117175613-117176689	A549	lung:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
44	POLR2A	chr12:117175459-117176498	GM12878	blood:	n/a	n/a
45	CTCF	chr12:117176300-117176450	GM12870	blood:	n/a	n/a
46	CTCF	chr12:117176360-117176510	GM12869	blood:	n/a	n/a
47	POLR2A	chr12:117175506-117176523	GM18505	blood:	n/a	n/a
48	USF2	chr12:117175565-117176471	GM12878	blood:	n/a	chr12:117176091-117176102
49	RCOR1	chr12:117175871-117176568	K562	blood:	n/a	n/a
50	TCF7L2	chr12:117175382-117176632	HCT-116	colon:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:117176367-117176417	HCT-116	colon:	n/a
2	chr12:117176367-117176417	HCPEpiC	choroid plexus:	n/a
3	chr12:117176367-117176417	NH-A	brain:	n/a
4	chr12:117176367-117176417	NHBE	bronchial:	n/a
5	chr12:117176367-117176417	HL-60	blood:	n/a
6	chr12:117176367-117176417	NT2-D1	testis:	n/a
7	chr12:117176367-117176417	HPAEpiC	pulmonary alveolar:	n/a
8	chr12:117176367-117176417	HepG2	liver:	n/a
9	chr12:117176367-117176417	HCM	heart:	n/a
10	chr12:117176367-117176417	LNCaP	prostate:	n/a
11	chr12:117176367-117176417	H1-hESC	embryonic stem cell:	embryo
12	chr12:117176367-117176417	HEK293	kidney:	embryo
13	chr12:117176367-117176417	GM12892	blood:	n/a
14	chr12:117176367-117176417	AG04449	skin:	fetal
15	chr12:117176367-117176417	Jurkat	blood:	n/a
16	chr12:117176367-117176417	GM12891	blood:	n/a
17	chr12:117176367-117176417	MCF-7	breast:	n/a
18	chr12:117176367-117176417	ovcar-3	ovarian:	n/a
19	chr12:117176367-117176417	NB4	blood:	n/a
20	chr12:117176367-117176417	AG09309	skin:	n/a
21	chr12:117176367-117176417	HEEpiC	esophagus:	n/a
22	chr12:117176367-117176417	Hela-S3	cervix:	n/a
23	chr12:117176367-117176417	AG09319	gingival:	n/a
24	chr12:117176367-117176417	IMR90	lung:	fetal
25	chr12:117176367-117176417	CMK	blood:	n/a
26	chr12:117176367-117176417	HRE	kidney:	n/a
27	chr12:117176367-117176417	AoSMC	blood vessel:	n/a
28	chr12:117176367-117176417	HIPEpiC	eye:	n/a
29	chr12:117176367-117176417	ProgFib	skin:	n/a
30	chr12:117176367-117176417	SK-N-SH_RA	brain:	n/a
31	chr12:117176367-117176417	HRPEpiC	eye:	n/a
32	chr12:117176367-117176417	BE2_C	brain:	n/a
33	chr12:117176367-117176417	U87	brain:	n/a
34	chr12:117176367-117176417	AG04450	lung:	fetal
35	chr12:117176367-117176417	T-47D	breast:	n/a
36	chr12:117176367-117176417	HUVEC	blood vessel:	n/a
37	chr12:117176367-117176417	GM06990	blood:	n/a
38	chr12:117176367-117176417	A549	lung:	n/a
39	chr12:117176367-117176417	BJ	skin:	n/a
40	chr12:117176367-117176417	RPTEC	kidney:	n/a
41	chr12:117176367-117176417	SKMC	muscle:	n/a
42	chr12:117176367-117176417	HNPCEpiC	eye:	n/a
43	chr12:117176367-117176417	HMEC	breast:	n/a
44	chr12:117176367-117176417	GM19239	blood:	n/a
45	chr12:117176367-117176417	SK-N-SH	brain:	n/a
46	chr12:117176367-117176417	AG10803	skin:	n/a
47	chr12:117176367-117176417	NHDF-neo	bronchial:	n/a
48	chr12:117176367-117176417	PANC-1	pancreas:	n/a
49	chr12:117176367-117176417	SAEC	small airway:	n/a
50	chr12:117176367-117176417	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:117174912..117176575-chr12:117346883..117348986,2	MCF-7	breast:
2	chr12:117174783..117176988-chr12:117316113..117318785,2	MCF-7	breast:
3	chr12:117155749..117159803-chr12:117174359..117177084,5	MCF-7	breast:

Variant related genes	Relation type
C12orf49	TF binding region
C12orf49	CpG island
ENSG00000135116	Chromatin interaction
ENSG00000111412	Chromatin interaction
ENSG00000174989	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2270619	0.84[EUR][1000 genomes]
rs2279695	0.84[EUR][1000 genomes]
rs3809192	0.85[ASN][1000 genomes]
rs3809193	0.93[AMR][1000 genomes]
rs4275719	0.81[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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048004	chr12:117170738-117219076	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv1039046	chr12:117170989-117225635	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117174000-117176600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:117174000-117176600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:117174000-117176600	Active TSS	Lung	lung
4	chr12:117174000-117177000	Active TSS	H9 Cell Line	embryonic stem cell
5	chr12:117174000-117177200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr12:117174200-117176400	Active TSS	HSMM	muscle
7	chr12:117174200-117176800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr12:117174200-117176800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:117174200-117177200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:117174400-117176400	Active TSS	NHDF-Ad	bronchial
11	chr12:117174400-117176600	Active TSS	Aorta	Aorta
12	chr12:117174400-117176600	Active TSS	Gastric	stomach
13	chr12:117174400-117176600	Active TSS	Right Atrium	heart
14	chr12:117174400-117177000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:117174400-117177000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:117174600-117176400	Active TSS	Fetal Lung	lung
17	chr12:117174600-117176400	Active TSS	Sigmoid Colon	Sigmoid Colon
18	chr12:117174600-117176600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr12:117174600-117176600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:117174600-117176600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:117174600-117176800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:117174600-117176800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr12:117174600-117176800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:117174600-117176800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:117174600-117176800	Active TSS	Fetal Kidney	kidney
26	chr12:117174800-117176400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:117174800-117176400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr12:117174800-117176400	Active TSS	Small Intestine	intestine
29	chr12:117174800-117176400	Active TSS	GM12878-XiMat	blood
30	chr12:117174800-117176400	Active TSS	Hela-S3	cervix
31	chr12:117174800-117176400	Active TSS	NHEK	skin
32	chr12:117174800-117176600	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:117174800-117176600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:117174800-117176600	Active TSS	A549	lung
35	chr12:117174800-117176800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:117174800-117176800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:117174800-117177000	Active TSS	Brain Angular Gyrus	brain
38	chr12:117174800-117177200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:117175000-117176400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr12:117175000-117176400	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr12:117175000-117176400	Active TSS	Fetal Intestine Large	intestine
42	chr12:117175000-117176600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:117175000-117176600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:117175000-117176600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:117175000-117176600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:117175000-117176600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:117175000-117176600	Active TSS	Fetal Heart	heart
48	chr12:117175000-117176600	Active TSS	Left Ventricle	heart
49	chr12:117175000-117176600	Active TSS	Ovary	ovary
50	chr12:117175000-117176600	Active TSS	Rectal Smooth Muscle	rectum

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