Variant report

Variant	rs34116679
Chromosome Location	chr12:48358057-48358058
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	GATA3	chr12:48357852-48358392	T-47D	breast:	n/a	n/a
2	MYC	chr12:48357967-48358120	K562	blood:	n/a	n/a
3	CTCF	chr12:48358040-48358190	HMEC	breast:	n/a	n/a
4	WRNIP1	chr12:48357874-48358497	GM12878	blood:	n/a	n/a
5	RAD21	chr12:48356736-48358455	SK-N-SH	brain:	n/a	chr12:48357701-48357713 chr12:48357250-48357269
6	NFIC	chr12:48357056-48358594	ECC-1	luminal epithelium:	n/a	chr12:48357541-48357557 chr12:48357540-48357557
7	SMARCC1	chr12:48357027-48358349	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:48358010-48358115	MCF-7	breast:	n/a	n/a
9	YY1	chr12:48357933-48358193	GM12878	blood:	n/a	n/a
10	CTCF	chr12:48357960-48358110	SK-N-SH_RA	brain:	n/a	n/a
11	TEAD4	chr12:48357856-48358310	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIN3AK20	chr12:48357916-48358157	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr12:48357898-48358306	K562	blood:	n/a	n/a
14	CTCF	chr12:48357980-48358130	AG04449	skin:	n/a	n/a
15	GATA3	chr12:48357878-48358461	T-47D	breast:	n/a	n/a
16	POLR2A	chr12:48357005-48358541	SK-N-MC	brain:	n/a	n/a
17	MAX	chr12:48357006-48358390	MCF-7	breast:	n/a	n/a
18	TCF12	chr12:48356881-48358078	A549	lung:	n/a	n/a
19	CTCF	chr12:48358000-48358150	Caco-2	colon:	n/a	n/a
20	SMC3	chr12:48356860-48358490	SK-N-SH	brain:	n/a	chr12:48357572-48357582
21	CTCF	chr12:48356634-48358309	A549	lung:	n/a	chr12:48357253-48357269 chr12:48357247-48357268 chr12:48357252-48357270 chr12:48357481-48357489 chr12:48357572-48357585
22	SMARCB1	chr12:48357054-48358198	Hela-S3	cervix:	n/a	n/a
23	CHD2	chr12:48358053-48358241	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:48357100-48358182	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr12:48357960-48358110	GM12873	blood:	n/a	n/a
26	TEAD4	chr12:48357884-48358362	K562	blood:	n/a	n/a
27	BHLHE40	chr12:48357877-48358362	K562	blood:	n/a	n/a
28	EP300	chr12:48357957-48358075	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:48357907-48358220	MCF-7	breast:	n/a	n/a
30	RAD21	chr12:48357898-48358194	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr12:48358046-48358195	K562	blood:	n/a	n/a
32	SIN3A	chr12:48356997-48358337	H1-hESC	embryonic stem cell:	n/a	chr12:48357581-48357592 chr12:48357246-48357257 chr12:48358317-48358330 chr12:48357052-48357060
33	GATA3	chr12:48357637-48358457	MCF-7	breast:	n/a	n/a
34	CTCF	chr12:48358020-48358170	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr12:48357960-48358110	HEK293	kidney:	n/a	n/a
36	CTCF	chr12:48357980-48358130	GM12873	blood:	n/a	n/a
37	YY1	chr12:48358002-48358252	SK-N-SH_RA	brain:	n/a	n/a
38	SRF	chr12:48357781-48358397	MCF-7	breast:	n/a	chr12:48358129-48358147
39	SRF	chr12:48357880-48358469	MCF-7	breast:	n/a	chr12:48358129-48358147
40	MAX	chr12:48356942-48358344	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr12:48358009-48358178	GM12878	blood:	n/a	n/a
42	ZBTB7A	chr12:48356986-48358355	ECC-1	luminal epithelium:	n/a	chr12:48357554-48357561 chr12:48357685-48357692
43	BHLHE40	chr12:48357983-48358330	HepG2	liver:	n/a	n/a
44	MAZ	chr12:48357903-48358206	GM12878	blood:	n/a	n/a
45	TCF12	chr12:48356984-48358308	ECC-1	luminal epithelium:	n/a	n/a
46	CTCF	chr12:48357960-48358110	GM12874	blood:	n/a	n/a
47	CTCF	chr12:48357980-48358130	HBMEC	blood vessel:	n/a	n/a
48	CTCF	chr12:48357960-48358110	Hela-S3	cervix:	n/a	n/a
49	MYC	chr12:48358003-48358270	MCF-7	breast:	n/a	n/a
50	MXI1	chr12:48357913-48358133	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48298691..48299776-chr12:48356759..48358181,8	MCF-7	breast:
2	chr12:48355845..48358792-chr12:48550018..48552863,2	K562	blood:
3	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
4	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
5	chr12:48099497..48101180-chr12:48357340..48359052,2	K562	blood:

Variant related genes	Relation type
TMEM106C	TF binding region
ENSG00000005175	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10467100	1.00[EUR][1000 genomes]
rs11168264	1.00[EUR][1000 genomes]
rs11168288	1.00[EUR][1000 genomes]
rs11168290	1.00[EUR][1000 genomes]
rs11168368	1.00[EUR][1000 genomes]
rs11574002	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574060	1.00[EUR][1000 genomes]
rs11830088	1.00[EUR][1000 genomes]
rs11833896	1.00[EUR][1000 genomes]
rs11835282	1.00[EUR][1000 genomes]
rs11835720	1.00[EUR][1000 genomes]
rs11836542	1.00[EUR][1000 genomes]
rs11838217	1.00[EUR][1000 genomes]
rs12297117	1.00[EUR][1000 genomes]
rs1793947	1.00[EUR][1000 genomes]
rs34120080	1.00[EUR][1000 genomes]
rs34698661	1.00[EUR][1000 genomes]
rs35445616	1.00[EUR][1000 genomes]
rs35902603	1.00[EUR][1000 genomes]
rs41272031	0.88[AFR][1000 genomes]
rs41272745	1.00[EUR][1000 genomes]
rs41272751	1.00[EUR][1000 genomes]
rs41272757	1.00[EUR][1000 genomes]
rs41272761	1.00[EUR][1000 genomes]
rs41272775	1.00[AMR][1000 genomes]
rs56265470	1.00[EUR][1000 genomes]
rs57550917	1.00[EUR][1000 genomes]
rs57783574	1.00[EUR][1000 genomes]
rs58279970	1.00[EUR][1000 genomes]
rs58573495	1.00[EUR][1000 genomes]
rs59339937	1.00[EUR][1000 genomes]
rs60556433	1.00[EUR][1000 genomes]
rs60894356	1.00[EUR][1000 genomes]
rs7316602	1.00[EUR][1000 genomes]
rs73297147	1.00[EUR][1000 genomes]
rs73297150	1.00[EUR][1000 genomes]
rs73297159	1.00[EUR][1000 genomes]
rs74085216	1.00[EUR][1000 genomes]
rs74085221	1.00[EUR][1000 genomes]
rs74086446	1.00[EUR][1000 genomes]
rs74086467	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088715	1.00[EUR][1000 genomes]
rs74088779	1.00[EUR][1000 genomes]
rs7954412	1.00[EUR][1000 genomes]
rs7967673	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48356800-48358400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr12:48357000-48358200	Active TSS	Aorta	Aorta
3	chr12:48357000-48358200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr12:48357000-48358400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:48357000-48358400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:48357000-48358400	Active TSS	Esophagus	oesophagus
7	chr12:48357200-48358200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:48357200-48358200	Active TSS	Fetal Intestine Large	intestine
9	chr12:48357200-48358200	Active TSS	Fetal Kidney	kidney
10	chr12:48357200-48358400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr12:48357200-48358400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:48357200-48358600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:48357400-48358200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:48357400-48358200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr12:48357400-48358200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:48357400-48358200	Flanking Active TSS	Fetal Muscle Trunk	muscle
17	chr12:48357400-48358400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr12:48357600-48358200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:48357600-48358200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:48357600-48358200	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr12:48357600-48358200	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr12:48357600-48358400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:48357600-48358400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr12:48357600-48358400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:48357600-48358400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:48357600-48358400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:48357600-48358400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:48357800-48358200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:48357800-48358200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:48357800-48358200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr12:48357800-48358200	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr12:48357800-48358200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:48357800-48358200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr12:48357800-48358200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:48357800-48358200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:48357800-48358200	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr12:48357800-48358200	Flanking Active TSS	HSMMtube	muscle
38	chr12:48357800-48358400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:48357800-48358400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr12:48357800-48358400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:48357800-48358400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr12:48357800-48358400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr12:48357800-48358400	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr12:48357800-48358400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:48357800-48358400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr12:48357800-48358400	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr12:48357800-48358400	Flanking Active TSS	Placenta	Placenta
48	chr12:48357800-48358400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr12:48357800-48358400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:48357800-48358400	Flanking Active TSS	HUVEC	blood vessel

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