Variant report

Variant	rs3809218
Chromosome Location	chr12:9066613-9066614
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	MXI1	chr12:9065508-9067028	H1-hESC	embryonic stem cell:	n/a	chr12:9066967-9066982 chr12:9066965-9066980
2	GABPA	chr12:9066560-9067229	MCF-7	breast:	n/a	chr12:9067107-9067116
3	TCF7L2	chr12:9066417-9066872	HEK293	kidney:	n/a	chr12:9066699-9066713 chr12:9066702-9066712 chr12:9066698-9066714 chr12:9066698-9066714 chr12:9066701-9066710
4	E2F6	chr12:9066301-9067032	H1-hESC	embryonic stem cell:	n/a	chr12:9066524-9066531 chr12:9066523-9066535 chr12:9066524-9066531 chr12:9066524-9066531 chr12:9066523-9066531
5	STAT3	chr12:9066544-9066784	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr12:9066541-9067007	SK-N-MC	brain:	n/a	n/a
7	CREB1	chr12:9066513-9067171	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr12:9066406-9066981	K562	blood:	n/a	chr12:9066967-9066976 chr12:9066971-9066980
9	TAF1	chr12:9066570-9067041	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr12:9066395-9067028	HUVEC	blood vessel:	n/a	n/a
11	ZMIZ1	chr12:9066385-9066896	K562	blood:	n/a	n/a
12	KAP1	chr12:9065591-9066967	HEK293	kidney:	n/a	n/a
13	POLR2A	chr12:9065519-9067177	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr12:9066613-9067001	HCT-116	colon:	n/a	n/a
15	GABPA	chr12:9066366-9067210	SK-N-SH	brain:	n/a	chr12:9067107-9067116
16	POLR2A	chr12:9066354-9067019	U87	brain:	n/a	n/a
17	E2F4	chr12:9066225-9066892	MCF10A-Er-Src	breast:	n/a	chr12:9066524-9066531 chr12:9066523-9066535 chr12:9066524-9066531 chr12:9066524-9066531 chr12:9066523-9066531
18	CHD2	chr12:9065219-9066991	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:9065499-9067183	H1-neurons	neurons:	n/a	n/a
20	TAF7	chr12:9064014-9067029	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr12:9066605-9067199	A549	lung:	n/a	chr12:9066967-9066976 chr12:9066971-9066980 chr12:9067093-9067103
22	MAZ	chr12:9066253-9067204	IMR90	lung:	n/a	chr12:9066967-9066976 chr12:9066971-9066980 chr12:9067093-9067103
23	MAZ	chr12:9066560-9067833	K562	blood:	n/a	chr12:9066967-9066976 chr12:9066971-9066980 chr12:9067093-9067103
24	TAF1	chr12:9066564-9067018	SK-N-SH	brain:	n/a	n/a
25	MAX	chr12:9066315-9067213	A549	lung:	n/a	chr12:9066967-9066976 chr12:9066971-9066980 chr12:9067093-9067103
26	JUND	chr12:9065438-9067003	H1-hESC	embryonic stem cell:	n/a	chr12:9065461-9065472 chr12:9065464-9065471 chr12:9065459-9065470 chr12:9065463-9065471 chr12:9066451-9066460
27	POLR2A	chr12:9066458-9067020	SK-N-SH	brain:	n/a	n/a
28	TAF1	chr12:9066511-9067006	H1-hESC	embryonic stem cell:	n/a	n/a
29	SP1	chr12:9066547-9067042	H1-hESC	embryonic stem cell:	n/a	chr12:9066776-9066787
30	TCF7L2	chr12:9066507-9066856	PANC-1	pancreas:	n/a	chr12:9066699-9066713 chr12:9066702-9066712 chr12:9066698-9066714 chr12:9066698-9066714 chr12:9066701-9066710
31	SIN3A	chr12:9064234-9069882	H1-hESC	embryonic stem cell:	n/a	chr12:9066956-9066965 chr12:9068258-9068267
32	POLR2A	chr12:9065227-9067927	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr12:9065322-9067165	H1-neurons	neurons:	n/a	chr12:9067106-9067119 chr12:9066955-9066965
34	POLR2A	chr12:9066529-9067008	MCF10A-Er-Src	breast:	n/a	n/a
35	GABPA	chr12:9066435-9067187	SK-N-SH	brain:	n/a	chr12:9067107-9067116
36	POLR2A	chr12:9066366-9067211	SK-N-MC	brain:	n/a	n/a
37	SIN3AK20	chr12:9066599-9066995	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr12:9066006-9067026	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr12:9066577-9066872	SK-N-SH	brain:	n/a	n/a
40	REST	chr12:9065539-9067070	H1-neurons	neurons:	n/a	chr12:9066955-9066965
41	TCF7L2	chr12:9066499-9067131	HCT-116	colon:	n/a	chr12:9066699-9066713 chr12:9066702-9066712 chr12:9066698-9066714 chr12:9066698-9066714 chr12:9066701-9066710
42	SMC3	chr12:9066606-9067006	Hela-S3	cervix:	n/a	n/a
43	TBP	chr12:9065230-9067100	H1-hESC	embryonic stem cell:	n/a	n/a
44	RCOR1	chr12:9066589-9067034	K562	blood:	n/a	n/a
45	GABPA	chr12:9066507-9067031	A549	lung:	n/a	n/a
46	GABPA	chr12:9066432-9067180	A549	lung:	n/a	chr12:9067107-9067116
47	MAX	chr12:9065557-9067078	H1-hESC	embryonic stem cell:	n/a	chr12:9066967-9066976 chr12:9066971-9066980
48	ELK1	chr12:9066611-9066939	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr12:9066540-9066690	GM12872	blood:	n/a	n/a
50	EP300	chr12:9066590-9067019	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9064962..9066827-chr12:9216213..9218614,2	MCF-7	breast:
2	chr12:9064351..9068260-chr12:9100706..9102986,3	MCF-7	breast:
3	chr12:9065799..9067529-chr12:9095135..9097465,2	MCF-7	breast:
4	chr12:9065401..9068009-chr12:9098811..9103435,5	MCF-7	breast:

Variant related genes	Relation type
PHC1	TF binding region
ENSG00000003056	Chromatin interaction
ENSG00000245105	Chromatin interaction
ENSG00000214851	Chromatin interaction
ENSG00000139187	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10771204	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10771216	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11047996	0.86[ASN][1000 genomes]
rs11048060	0.84[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1805740	0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1805741	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1805778	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4882966	0.90[ASN][1000 genomes]
rs4882967	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4882968	0.89[ASN][1000 genomes]
rs4882969	0.88[ASN][1000 genomes]
rs4883197	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4883198	0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4883199	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4883200	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7297194	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7309772	0.86[ASN][1000 genomes]
rs7312166	0.81[ASN][1000 genomes]
rs7312676	0.89[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3809218	RPL13P5	cis	cerebellum	SCAN
rs3809218	PHC1	cis	Esophagus Muscularis	GTEx
rs3809218	KLRB1	cis	cerebellum	SCAN
rs3809218	M6PR	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9063800-9069600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:9064600-9070200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr12:9064800-9069400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:9064800-9069600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr12:9065200-9070200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr12:9065200-9070200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:9065600-9068000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:9065600-9068000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:9065600-9068400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr12:9065600-9069400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:9065600-9069800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:9065800-9066800	Flanking Active TSS	NHEK	skin
13	chr12:9065800-9067600	Active TSS	Fetal Brain Female	brain
14	chr12:9066000-9066800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr12:9066000-9066800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:9066000-9066800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:9066000-9066800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr12:9066000-9066800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:9066000-9066800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr12:9066000-9066800	Flanking Active TSS	HMEC	breast
21	chr12:9066000-9066800	Flanking Active TSS	HUVEC	blood vessel
22	chr12:9066000-9066800	Flanking Active TSS	NH-A	brain
23	chr12:9066000-9067000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr12:9066000-9067000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr12:9066000-9067600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:9066000-9067600	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:9066000-9067800	Active TSS	Brain Cingulate Gyrus	brain
28	chr12:9066000-9068000	Active TSS	Aorta	Aorta
29	chr12:9066000-9068000	Active TSS	Esophagus	oesophagus
30	chr12:9066000-9068000	Active TSS	Left Ventricle	heart
31	chr12:9066000-9068000	Active TSS	Psoas Muscle	Psoas
32	chr12:9066000-9068400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:9066000-9068600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:9066000-9068800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:9066000-9069000	Active TSS	Right Atrium	heart
36	chr12:9066000-9069600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:9066200-9066800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:9066200-9066800	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr12:9066200-9066800	Flanking Active TSS	A549	lung
40	chr12:9066200-9066800	Flanking Active TSS	K562	blood
41	chr12:9066200-9066800	Flanking Active TSS	Osteobl	bone
42	chr12:9066200-9067000	Flanking Active TSS	Dnd41	blood
43	chr12:9066200-9067800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:9066200-9067800	Active TSS	Fetal Brain Male	brain
45	chr12:9066200-9067800	Active TSS	Fetal Muscle Leg	muscle
46	chr12:9066200-9067800	Active TSS	Right Ventricle	heart
47	chr12:9066200-9067800	Active TSS	Stomach Smooth Muscle	stomach
48	chr12:9066200-9068000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:9066200-9068000	Active TSS	Brain Germinal Matrix	brain
50	chr12:9066200-9068000	Active TSS	Fetal Lung	lung

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