Variant report

Variant	rs3809192
Chromosome Location	chr12:117176552-117176553
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	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
3	POLR2A	chr12:117175415-117176619	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr12:117175593-117176605	SK-N-SH	brain:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
5	RELA	chr12:117175636-117176599	GM10847	blood:	n/a	n/a
6	FOXM1	chr12:117175737-117176584	GM12878	blood:	n/a	n/a
7	SMC3	chr12:117175538-117176605	Hela-S3	cervix:	n/a	n/a
8	MAX	chr12:117175468-117176638	MCF-7	breast:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
9	RCOR1	chr12:117175757-117176573	Hela-S3	cervix:	n/a	n/a
10	GABPA	chr12:117175544-117176638	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:117175307-117176591	Raji	blood:	n/a	n/a
12	STAT5A	chr12:117175737-117176590	GM12878	blood:	n/a	chr12:117175980-117175992
13	MXI1	chr12:117175449-117176658	GM12878	blood:	n/a	chr12:117175866-117175875
14	TCF7L2	chr12:117175868-117176619	Hela-S3	cervix:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
15	MAX	chr12:117175613-117176689	A549	lung:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
16	RCOR1	chr12:117175871-117176568	K562	blood:	n/a	n/a
17	TCF7L2	chr12:117175382-117176632	HCT-116	colon:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
18	FOXM1	chr12:117175713-117176659	MCF-7	breast:	n/a	n/a
19	GABPA	chr12:117175771-117176556	A549	lung:	n/a	n/a
20	RAD21	chr12:117176082-117176555	HepG2	liver:	n/a	n/a
21	RFX5	chr12:117174654-117177903	SK-N-SH	brain:	n/a	chr12:117174964-117174973 chr12:117174962-117174976 chr12:117176118-117176127
22	BRCA1	chr12:117175433-117176578	Hela-S3	cervix:	n/a	n/a
23	SP1	chr12:117175586-117176595	A549	lung:	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
24	TCF7L2	chr12:117176250-117176713	HEK293	kidney:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
25	CREB1	chr12:117175634-117176608	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAZ	chr12:117174770-117176667	IMR90	lung:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
27	NFYB	chr12:117175580-117176621	GM12878	blood:	n/a	chr12:117175960-117175975 chr12:117175961-117175975 chr12:117175960-117175975
28	MAX	chr12:117175680-117176553	H1-hESC	embryonic stem cell:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
29	MAX	chr12:117175459-117176772	A549	lung:	n/a	chr12:117175865-117175874 chr12:117176692-117176702 chr12:117175863-117175872 chr12:117175864-117175875
30	MAX	chr12:117175054-117176672	HCT-116	colon:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
31	POLR2A	chr12:117175542-117176579	GM18951	blood:	n/a	n/a
32	POLR2A	chr12:117175568-117176727	GM12891	blood:	n/a	n/a
33	SIN3A	chr12:117174905-117176556	H1-hESC	embryonic stem cell:	n/a	chr12:117175866-117175875 chr12:117175894-117175905
34	SIN3AK20	chr12:117175365-117176794	MCF-7	breast:	n/a	n/a
35	FOXM1	chr12:117175692-117176663	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr12:117175573-117176580	H1-neurons	neurons:	n/a	n/a
37	MXI1	chr12:117174549-117177000	SK-N-SH	brain:	n/a	chr12:117175866-117175875
38	TCF7L2	chr12:117175980-117176663	MCF-7	breast:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
39	TCF7L2	chr12:117175839-117176600	PANC-1	pancreas:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
40	RAD21	chr12:117176156-117176561	H1-hESC	embryonic stem cell:	n/a	n/a
41	SP1	chr12:117175219-117176627	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
42	HDAC2	chr12:117175734-117176688	MCF-7	breast:	n/a	chr12:117176196-117176210 chr12:117176192-117176206 chr12:117176195-117176209 chr12:117176194-117176208 chr12:117176199-117176213
43	E2F6	chr12:117175776-117176581	A549	lung:	n/a	chr12:117175886-117175895
44	REST	chr12:117175397-117176888	H1-neurons	neurons:	n/a	chr12:117176100-117176113
45	MAX	chr12:117175774-117176594	ECC-1	luminal epithelium:	n/a	chr12:117175865-117175874 chr12:117175863-117175872 chr12:117175864-117175875
46	ELF1	chr12:117175449-117176588	GM12878	blood:	n/a	chr12:117175885-117175897
47	CREB1	chr12:117175404-117176623	GM12878	blood:	n/a	n/a
48	CTCF	chr12:117176340-117176570	GM12872	blood:	n/a	n/a
49	RCOR1	chr12:117175063-117176577	K562	blood:	n/a	n/a
50	FOXM1	chr12:117175785-117176559	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:117174912..117176575-chr12:117346883..117348986,2	MCF-7	breast:
2	chr12:117172847..117175842-chr12:117176495..117179141,3	MCF-7	breast:
3	chr12:117174783..117176988-chr12:117316113..117318785,2	MCF-7	breast:
4	chr12:117155749..117159803-chr12:117174359..117177084,5	MCF-7	breast:

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

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11832734	0.86[EUR][1000 genomes]
rs2279695	0.84[CHD][hapmap]
rs3809191	0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3809192	OR6S1	trans	cerebellum	SCAN

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	chr12:117174200-117176800	Active TSS	H1 Cell Line	embryonic stem cell
7	chr12:117174200-117176800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:117174200-117177200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:117174400-117176600	Active TSS	Aorta	Aorta
10	chr12:117174400-117176600	Active TSS	Gastric	stomach
11	chr12:117174400-117176600	Active TSS	Right Atrium	heart
12	chr12:117174400-117177000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr12:117174400-117177000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:117174600-117176600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr12:117174600-117176600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:117174600-117176600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:117174600-117176800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:117174600-117176800	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr12:117174600-117176800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:117174600-117176800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:117174600-117176800	Active TSS	Fetal Kidney	kidney
22	chr12:117174800-117176600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:117174800-117176600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:117174800-117176600	Active TSS	A549	lung
25	chr12:117174800-117176800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:117174800-117176800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:117174800-117177000	Active TSS	Brain Angular Gyrus	brain
28	chr12:117174800-117177200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:117175000-117176600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:117175000-117176600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:117175000-117176600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:117175000-117176600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:117175000-117176600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:117175000-117176600	Active TSS	Fetal Heart	heart
35	chr12:117175000-117176600	Active TSS	Left Ventricle	heart
36	chr12:117175000-117176600	Active TSS	Ovary	ovary
37	chr12:117175000-117176600	Active TSS	Rectal Smooth Muscle	rectum
38	chr12:117175000-117176800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:117175000-117176800	Active TSS	Brain Anterior Caudate	brain
40	chr12:117175000-117176800	Active TSS	Brain Cingulate Gyrus	brain
41	chr12:117175000-117176800	Active TSS	NH-A	brain
42	chr12:117175000-117177000	Active TSS	NHLF	lung
43	chr12:117175200-117176600	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr12:117175200-117176600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr12:117175200-117176600	Active TSS	Brain Substantia Nigra	brain
46	chr12:117175200-117176600	Active TSS	Fetal Brain Male	brain
47	chr12:117175200-117176600	Active TSS	Fetal Brain Female	brain
48	chr12:117175200-117176600	Active TSS	Psoas Muscle	Psoas
49	chr12:117175400-117176600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:117175400-117176800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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