Variant report

Variant	rs775325
Chromosome Location	chr12:57940749-57940750
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	MAX	chr12:57940550-57941316	ECC-1	luminal epithelium:	n/a	n/a
2	SRF	chr12:57940749-57941299	ECC-1	luminal epithelium:	n/a	n/a
3	PML	chr12:57940714-57941215	K562	blood:	n/a	n/a
4	ZKSCAN1	chr12:57940749-57941236	Hela-S3	cervix:	n/a	n/a
5	YY1	chr12:57940707-57941239	K562	blood:	n/a	chr12:57940847-57940856
6	HCFC1	chr12:57940618-57941369	K562	blood:	n/a	n/a
7	BCLAF1	chr12:57940217-57940753	GM12878	blood:	n/a	n/a
8	PML	chr12:57940172-57941394	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:57939907-57941301	U87	brain:	n/a	n/a
10	POLR2A	chr12:57940354-57941101	HCT-116	colon:	n/a	n/a
11	ZBTB33	chr12:57940682-57941314	A549	lung:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
12	TBL1XR1	chr12:57940744-57941251	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:57940562-57941154	A549	lung:	n/a	n/a
14	MAZ	chr12:57939889-57941309	K562	blood:	n/a	n/a
15	POLR2A	chr12:57940499-57941199	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr12:57940736-57941328	SK-N-MC	brain:	n/a	n/a
17	SP4	chr12:57940619-57941159	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:57940705-57941317	HCT-116	colon:	n/a	n/a
19	MAX	chr12:57940739-57941257	A549	lung:	n/a	n/a
20	ZBTB33	chr12:57940726-57941208	GM12878	blood:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
21	POLR2A	chr12:57940743-57941222	Raji	blood:	n/a	n/a
22	TAF1	chr12:57940410-57941110	K562	blood:	n/a	n/a
23	SRF	chr12:57940661-57941422	HCT-116	colon:	n/a	n/a
24	ZBTB33	chr12:57940015-57941446	A549	lung:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
25	SIN3AK20	chr12:57940265-57941233	SK-N-SH	brain:	n/a	n/a
26	ELF1	chr12:57940467-57941222	GM12878	blood:	n/a	chr12:57940963-57940976 chr12:57940847-57940856
27	UBTF	chr12:57940433-57941197	K562	blood:	n/a	n/a
28	POLR2A	chr12:57940331-57941187	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr12:57939877-57941250	K562	blood:	n/a	n/a
30	YY1	chr12:57940186-57941195	GM12892	blood:	n/a	chr12:57940847-57940856
31	POLR2A	chr12:57940749-57941120	MCF-7	breast:	n/a	n/a
32	POLR2A	chr12:57939818-57941257	HUVEC	blood vessel:	n/a	n/a
33	TCF12	chr12:57939800-57941009	A549	lung:	n/a	chr12:57940018-57940027 chr12:57940006-57940016
34	CTCF	chr12:57940700-57940850	GM12872	blood:	n/a	chr12:57940716-57940729
35	GABPA	chr12:57940363-57940883	A549	lung:	n/a	n/a
36	SIN3AK20	chr12:57940184-57941159	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr12:57940480-57940757	K562	blood:	n/a	chr12:57940716-57940729 chr12:57940617-57940630
38	TAF1	chr12:57940189-57941173	H1-hESC	embryonic stem cell:	n/a	n/a
39	YY1	chr12:57940714-57941195	H1-hESC	embryonic stem cell:	n/a	chr12:57940847-57940856
40	POLR2A	chr12:57939600-57941148	H1-hESC	embryonic stem cell:	n/a	n/a
41	MTA3	chr12:57939677-57941261	GM12878	blood:	n/a	n/a
42	ZBTB33	chr12:57940611-57941417	HCT-116	colon:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
43	ZBTB33	chr12:57940587-57941391	SK-N-SH	brain:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
44	YY1	chr12:57940341-57941208	K562	blood:	n/a	chr12:57940847-57940856
45	TCF12	chr12:57940483-57941355	ECC-1	luminal epithelium:	n/a	n/a
46	ZBTB33	chr12:57940740-57941221	K562	blood:	n/a	chr12:57940975-57940984 chr12:57941015-57941025 chr12:57941009-57941024 chr12:57940970-57940985
47	POLR2A	chr12:57939775-57941262	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr12:57939749-57941238	GM12892	blood:	n/a	n/a
49	CCNT2	chr12:57940615-57941193	K562	blood:	n/a	n/a
50	POLR2A	chr12:57940403-57941116	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57940714..57942505-chr12:58117953..58120525,2	MCF-7	breast:
2	chr12:57881658..57883601-chr12:57939659..57941613,2	MCF-7	breast:
3	chr12:57938852..57941348-chr12:58005104..58006975,2	K562	blood:
4	chr12:57938950..57942640-chr12:57942750..57946701,7	K562	blood:
5	chr12:57940164..57942070-chr12:58025601..58028102,2	MCF-7	breast:
6	chr12:57940172..57943060-chr12:58144511..58146770,2	K562	blood:
7	chr12:57939429..57943777-chr12:57984797..57987088,3	K562	blood:
8	chr12:57940234..57941945-chr12:57983939..57986632,2	MCF-7	breast:
9	chr12:57939451..57941325-chr12:58024374..58027583,3	K562	blood:
10	chr12:57939583..57941703-chr12:58002111..58004794,2	K562	blood:
11	chr12:57939918..57942387-chr12:58138816..58141058,2	K562	blood:
12	chr12:57940214..57942562-chr12:57943543..57945159,2	MCF-7	breast:
13	chr12:57881482..57885096-chr12:57938469..57941069,3	K562	blood:
14	chr12:57929188..57932764-chr12:57939481..57941098,3	MCF-7	breast:
15	chr12:57940405..57942301-chr12:57997757..58000737,2	MCF-7	breast:

Variant related genes	Relation type
KIF5A	TF binding region
DCTN2	TF binding region
ENSG00000240771	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000123329	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000178498	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000155980	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1148550	1.00[EUR][1000 genomes]
rs1284467	1.00[EUR][1000 genomes]
rs1679366	1.00[EUR][1000 genomes]
rs2620680	1.00[EUR][1000 genomes]
rs537161	1.00[EUR][1000 genomes]
rs59235552	1.00[EUR][1000 genomes]
rs60374392	1.00[EUR][1000 genomes]
rs703833	1.00[EUR][1000 genomes]
rs703840	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs776340	1.00[EUR][1000 genomes]
rs7973639	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
2	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
9	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
10	nsv1053930	chr12:57921188-57969659	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57938600-57940800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr12:57939600-57941400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:57939800-57941200	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:57939800-57941400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:57939800-57941400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:57940000-57941000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:57940000-57941000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr12:57940000-57941000	Active TSS	Placenta Amnion	Placenta Amnion
9	chr12:57940000-57941000	Active TSS	Small Intestine	intestine
10	chr12:57940000-57941600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr12:57940000-57941600	Active TSS	Aorta	Aorta
12	chr12:57940200-57940800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr12:57940200-57940800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:57940200-57940800	Bivalent/Poised TSS	HepG2	liver
15	chr12:57940200-57941000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr12:57940200-57941000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:57940200-57941000	Active TSS	Esophagus	oesophagus
18	chr12:57940200-57941000	Active TSS	Left Ventricle	heart
19	chr12:57940200-57941000	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr12:57940200-57941200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr12:57940200-57941200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:57940200-57941200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:57940200-57941200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:57940200-57941200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:57940200-57941200	Active TSS	Muscle Satellite Cultured Cells	--
26	chr12:57940200-57941200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:57940200-57941200	Active TSS	Colon Smooth Muscle	Colon
28	chr12:57940200-57941200	Active TSS	Fetal Heart	heart
29	chr12:57940200-57941200	Active TSS	Fetal Kidney	kidney
30	chr12:57940200-57941200	Active TSS	Fetal Stomach	stomach
31	chr12:57940200-57941200	Active TSS	GM12878-XiMat	blood
32	chr12:57940200-57941200	Active TSS	Hela-S3	cervix
33	chr12:57940200-57941200	Active TSS	HMEC	breast
34	chr12:57940200-57941200	Active TSS	HSMM	muscle
35	chr12:57940200-57941400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:57940200-57941400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr12:57940200-57941400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:57940200-57941400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:57940200-57941400	Active TSS	Psoas Muscle	Psoas
40	chr12:57940200-57941400	Active TSS	A549	lung
41	chr12:57940200-57941400	Active TSS	NHDF-Ad	bronchial
42	chr12:57940400-57940800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:57940400-57941000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:57940400-57941000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:57940400-57941000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:57940400-57941000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:57940400-57941000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:57940400-57941000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:57940400-57941000	Active TSS	Fetal Thymus	thymus
50	chr12:57940400-57941000	Active TSS	Gastric	stomach

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