Variant report

Variant	rs7297878
Chromosome Location	chr12:1869916-1869917
allele	A/C
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	SMC3	chr12:1869883-1870188	HepG2	liver:	n/a	n/a
2	FOS	chr12:1869864-1870243	MCF10A-Er-Src	breast:	n/a	n/a
3	MYBL2	chr12:1869751-1870173	HepG2	liver:	n/a	n/a
4	FOSL2	chr12:1869840-1870249	HepG2	liver:	n/a	n/a
5	MXI1	chr12:1869915-1870226	HepG2	liver:	n/a	n/a
6	CEBPB	chr12:1869695-1870374	HCT-116	colon:	n/a	chr12:1870000-1870011
7	JUN	chr12:1869446-1870200	K562	blood:	n/a	n/a
8	FOXA2	chr12:1869825-1870185	HepG2	liver:	n/a	n/a
9	FOS	chr12:1869863-1870228	MCF10A-Er-Src	breast:	n/a	n/a
10	HDAC2	chr12:1869816-1870234	HepG2	liver:	n/a	n/a
11	FOXA1	chr12:1869827-1870175	HepG2	liver:	n/a	n/a
12	RXRA	chr12:1869777-1870161	HepG2	liver:	n/a	n/a
13	MYBL2	chr12:1869468-1870444	HepG2	liver:	n/a	n/a
14	NR2F2	chr12:1869898-1870277	K562	blood:	n/a	n/a
15	MAX	chr12:1869737-1870337	A549	lung:	n/a	n/a
16	SP1	chr12:1869647-1870217	HepG2	liver:	n/a	n/a
17	CEBPB	chr12:1869888-1870202	HepG2	liver:	n/a	chr12:1870000-1870011
18	JUND	chr12:1869688-1870363	HCT-116	colon:	n/a	chr12:1870047-1870058
19	EP300	chr12:1869748-1870221	Hela-S3	cervix:	n/a	n/a
20	TBP	chr12:1869729-1870262	Hela-S3	cervix:	n/a	n/a
21	TCF12	chr12:1869749-1870389	SK-N-SH	brain:	n/a	n/a
22	MAFF	chr12:1869889-1870199	HepG2	liver:	n/a	n/a
23	FOSL1	chr12:1869756-1870369	HCT-116	colon:	n/a	n/a
24	MAFK	chr12:1869909-1870185	HepG2	liver:	n/a	n/a
25	TCF7L2	chr12:1869916-1870174	Hela-S3	cervix:	n/a	n/a
26	GATA3	chr12:1869761-1870203	SK-N-SH	brain:	n/a	n/a
27	CEBPB	chr12:1869811-1870266	Hela-S3	cervix:	n/a	chr12:1870000-1870011
28	NFIC	chr12:1869562-1870385	HepG2	liver:	n/a	n/a
29	CHD2	chr12:1869893-1870198	Hela-S3	cervix:	n/a	n/a
30	JUND	chr12:1869828-1870204	SK-N-SH	brain:	n/a	chr12:1870047-1870058
31	TEAD4	chr12:1869623-1870344	HepG2	liver:	n/a	n/a
32	CEBPB	chr12:1869890-1870174	HepG2	liver:	n/a	chr12:1870000-1870011
33	MAX	chr12:1869813-1870228	Hela-S3	cervix:	n/a	n/a
34	FOXA1	chr12:1869692-1870243	HepG2	liver:	n/a	n/a
35	STAT3	chr12:1869866-1870166	MCF10A-Er-Src	breast:	n/a	n/a
36	CEBPB	chr12:1869659-1870236	A549	lung:	n/a	chr12:1870000-1870011
37	FOS	chr12:1869848-1870220	MCF10A-Er-Src	breast:	n/a	n/a
38	JUN	chr12:1869864-1870193	Hela-S3	cervix:	n/a	n/a
39	FOSL1	chr12:1869813-1870414	HCT-116	colon:	n/a	n/a
40	EP300	chr12:1869719-1870189	HepG2	liver:	n/a	n/a
41	RFX5	chr12:1869780-1870262	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr12:1869871-1870193	HCT-116	colon:	n/a	n/a
43	MAX	chr12:1869760-1870229	A549	lung:	n/a	n/a
44	STAT3	chr12:1869916-1870192	MCF10A-Er-Src	breast:	n/a	n/a
45	FOXA1	chr12:1869756-1870280	HepG2	liver:	n/a	n/a
46	HNF4A	chr12:1869873-1870229	HepG2	liver:	n/a	n/a
47	TCF12	chr12:1869690-1870354	A549	lung:	n/a	n/a
48	ZKSCAN1	chr12:1869889-1870187	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr12:1869869-1870155	MCF-7	breast:	n/a	n/a
50	EP300	chr12:1869621-1870296	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1805184..1807328-chr12:1869608..1872383,2	K562	blood:

Variant related genes	Relation type
RPS4XP14	TF binding region
ENSG00000271500	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11061904	1.00[EUR][1000 genomes]
rs1860049	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2041059	1.00[EUR][1000 genomes]
rs2108398	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2369974	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2370054	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35510932	1.00[EUR][1000 genomes]
rs4765838	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4766411	1.00[EUR][1000 genomes]
rs4766420	1.00[EUR][1000 genomes]
rs56369812	1.00[EUR][1000 genomes]
rs6489321	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6489325	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7133749	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7135229	1.00[EUR][1000 genomes]
rs7136278	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs7304843	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7308757	1.00[EUR][1000 genomes]
rs7314133	1.00[EUR][1000 genomes]
rs74061311	1.00[EUR][1000 genomes]
rs74061331	1.00[EUR][1000 genomes]
rs74061332	1.00[EUR][1000 genomes]
rs758026	1.00[EUR][1000 genomes]
rs758027	0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs758169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7957003	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7962777	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7964434	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1038425	chr12:1857052-1902302	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
2	chr12:1826000-1885400	Weak transcription	NH-A	brain
3	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
5	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
6	chr12:1850200-1885200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:1850400-1870400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:1850400-1904800	Weak transcription	Fetal Kidney	kidney
9	chr12:1850800-1885200	Weak transcription	Right Ventricle	heart
10	chr12:1851800-1876600	Weak transcription	Stomach Mucosa	stomach
11	chr12:1854600-1870400	Weak transcription	HSMMtube	muscle
12	chr12:1856600-1872000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:1857200-1870000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:1857200-1892800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:1857200-1893400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:1862000-1894800	Weak transcription	Colonic Mucosa	Colon
17	chr12:1862600-1874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:1863000-1882000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:1863400-1870200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:1863400-1871400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:1863400-1871400	Strong transcription	GM12878-XiMat	blood
22	chr12:1863400-1871400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:1863400-1872600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:1864800-1879800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:1864800-1882200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:1864800-1885400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:1865000-1885200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:1865800-1870000	Strong transcription	Primary B cells from cord blood	blood
29	chr12:1865800-1871400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:1866000-1871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:1866800-1871000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:1866800-1875000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr12:1866800-1883000	Weak transcription	Fetal Heart	heart
34	chr12:1867000-1871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:1867000-1882000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:1867000-1882000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:1867000-1890200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:1867200-1870400	Weak transcription	Psoas Muscle	Psoas
39	chr12:1867200-1870400	Enhancers	HepG2	liver
40	chr12:1867200-1871000	Weak transcription	Liver	Liver
41	chr12:1867200-1871400	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:1867200-1872200	Enhancers	Brain Hippocampus Middle	brain
43	chr12:1867200-1878000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:1867200-1878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:1867200-1878600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:1867200-1878800	Weak transcription	Fetal Intestine Small	intestine
47	chr12:1867200-1878800	Weak transcription	Lung	lung
48	chr12:1867200-1879200	Weak transcription	Gastric	stomach
49	chr12:1867200-1879200	Weak transcription	Left Ventricle	heart
50	chr12:1867200-1880200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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