Variant report

Variant	rs73593729
Chromosome Location	chr12:1926018-1926019
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	NFATC1	chr12:1925684-1926266	GM12878	blood:	n/a	n/a
2	SP1	chr12:1925018-1926128	HepG2	liver:	n/a	n/a
3	CTCF	chr12:1925900-1926050	HepG2	liver:	n/a	n/a
4	FOXA2	chr12:1925710-1926020	HepG2	liver:	n/a	n/a
5	NFIC	chr12:1925815-1926198	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:1925544-1926140	H1-neurons	neurons:	n/a	n/a
7	MYC	chr12:1925959-1926093	NB4	blood:	n/a	chr12:1926066-1926076 chr12:1926005-1926015
8	POLR2A	chr12:1925553-1926132	H1-neurons	neurons:	n/a	n/a
9	MBD4	chr12:1925424-1926119	HepG2	liver:	n/a	n/a
10	BHLHE40	chr12:1925707-1926113	K562	blood:	n/a	n/a
11	REST	chr12:1925079-1926221	H1-neurons	neurons:	n/a	chr12:1925852-1925872
12	SP1	chr12:1925875-1926068	HepG2	liver:	n/a	n/a
13	BCL3	chr12:1925781-1926303	GM12878	blood:	n/a	n/a
14	BCL3	chr12:1925752-1926306	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:1925849-1926102	HepG2	liver:	n/a	n/a
16	MAX	chr12:1925736-1926202	NB4	blood:	n/a	chr12:1926066-1926076 chr12:1926005-1926015
17	TCF3	chr12:1925784-1926257	GM12878	blood:	n/a	n/a
18	NFATC1	chr12:1925690-1926202	GM12878	blood:	n/a	n/a
19	REST	chr12:1925826-1926099	SK-N-SH	brain:	n/a	chr12:1925852-1925872
20	TCF3	chr12:1925868-1926173	GM12878	blood:	n/a	n/a
21	PBX3	chr12:1925799-1926163	GM12878	blood:	n/a	n/a
22	MYC	chr12:1925978-1926040	GM12878	blood:	n/a	chr12:1926005-1926015
23	CTCF	chr12:1925920-1926070	Caco-2	colon:	n/a	n/a
24	TCF12	chr12:1925895-1926195	HepG2	liver:	n/a	n/a
25	POLR2A	chr12:1925974-1926084	MCF-7	breast:	n/a	n/a
26	STAT5A	chr12:1925795-1926228	GM12878	blood:	n/a	n/a
27	MXI1	chr12:1925578-1926195	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:1925954-1926100	MCF-7	breast:	n/a	n/a
29	POLR2A	chr12:1925896-1926094	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1925102..1928805-chr12:1946979..1949915,3	MCF-7	breast:
2	chr12:1915615..1917986-chr12:1924786..1926838,2	K562	blood:
3	chr12:1923066..1926339-chr12:1927484..1932040,5	MCF-7	breast:

Variant related genes	Relation type
LRTM2	TF binding region
ENSG00000166159	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs57568326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57988383	1.00[AMR][1000 genomes]
rs58647180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58865324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59012815	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv556996	chr12:1891372-1934920	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv898592	chr12:1901485-1937801	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv468965	chr12:1907853-1931396	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv556997	chr12:1907853-1931396	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv468966	chr12:1907853-1933553	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv556998	chr12:1907853-1933553	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv470259	chr12:1907853-1945042	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv518013	chr12:1914273-1952990	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv898594	chr12:1916838-1952990	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv898595	chr12:1916838-1962759	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv898596	chr12:1923040-1962759	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
18	esv3340160	chr12:1923891-1928089	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1905600-1928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:1920000-1939400	Weak transcription	Gastric	stomach
3	chr12:1924800-1926600	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr12:1925000-1926200	Enhancers	Fetal Intestine Small	intestine
5	chr12:1925000-1926200	Flanking Active TSS	HepG2	liver
6	chr12:1925400-1926200	Bivalent Enhancer	Fetal Heart	heart
7	chr12:1925600-1926400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:1925800-1926200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:1925800-1926200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:1925800-1926200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
11	chr12:1925800-1926400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:1925800-1926600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
13	chr12:1926000-1926200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:1926000-1926200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:1926000-1926200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:1926000-1926200	Bivalent Enhancer	Fetal Brain Male	brain
17	chr12:1926000-1926200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
18	chr12:1926000-1926200	Bivalent Enhancer	K562	blood

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