Variant report

Variant	rs560612980
Chromosome Location	chr4:166248213-166248214
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	POLR2A	chr4:166247871-166251222	HepG2	liver:	n/a	n/a
2	MAX	chr4:166248148-166249148	HepG2	liver:	n/a	chr4:166248947-166248957 chr4:166248570-166248580
3	POLR2A	chr4:166247836-166249651	GM19099	blood:	n/a	n/a
4	MXI1	chr4:166248011-166249431	HepG2	liver:	n/a	chr4:166248519-166248534 chr4:166248521-166248536
5	POLR2A	chr4:166247962-166249410	SK-N-SH	brain:	n/a	n/a
6	ATF2	chr4:166248110-166248579	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:166248083-166249242	HCT-116	colon:	n/a	n/a
8	GATA1	chr4:166248117-166249450	PBDE	blood:	n/a	n/a
9	POLR2A	chr4:166247947-166248254	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr4:166248198-166248624	U87	brain:	n/a	n/a
11	POLR2A	chr4:166247986-166249373	GM19193	blood:	n/a	n/a
12	EGR1	chr4:166247936-166249110	ECC-1	luminal epithelium:	n/a	chr4:166248570-166248583 chr4:166248569-166248584 chr4:166248040-166248054 chr4:166248570-166248583
13	MAFK	chr4:166248160-166248625	K562	blood:	n/a	n/a
14	TBP	chr4:166248142-166249131	HepG2	liver:	n/a	n/a
15	POLR2A	chr4:166247554-166249174	SK-N-SH	brain:	n/a	n/a
16	ARID3A	chr4:166248161-166249019	K562	blood:	n/a	n/a
17	RCOR1	chr4:166248080-166249569	K562	blood:	n/a	n/a
18	NR2F2	chr4:166247900-166248932	K562	blood:	n/a	n/a
19	POLR2A	chr4:166246756-166254107	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr4:166248048-166249482	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr4:166247768-166249353	H1-hESC	embryonic stem cell:	n/a	n/a
22	STAT1	chr4:166248116-166248402	GM12878	blood:	n/a	chr4:166248248-166248256
23	CHD2	chr4:166248116-166249243	Hela-S3	cervix:	n/a	n/a
24	ARID3A	chr4:166248159-166248461	HepG2	liver:	n/a	n/a
25	POLR2A	chr4:166248080-166249397	K562	blood:	n/a	n/a
26	POLR2A	chr4:166247914-166249608	H1-neurons	neurons:	n/a	n/a
27	TBP	chr4:166247738-166248973	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr4:166248050-166248645	HepG2	liver:	n/a	n/a
29	EGR1	chr4:166247853-166248234	K562	blood:	n/a	chr4:166248040-166248054
30	MYC	chr4:166247965-166249280	MCF10A-Er-Src	breast:	n/a	chr4:166248947-166248957 chr4:166248570-166248580
31	POLR2A	chr4:166247782-166250685	HepG2	liver:	n/a	n/a
32	EP300	chr4:166248203-166249243	GM12878	blood:	n/a	chr4:166249000-166249016 chr4:166248457-166248466
33	FOXM1	chr4:166248112-166249107	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr4:166248019-166249030	GM12878	blood:	n/a	n/a
35	CHD1	chr4:166247763-166249723	GM12878	blood:	n/a	n/a
36	EP300	chr4:166248015-166249078	HepG2	liver:	n/a	chr4:166249000-166249016 chr4:166248457-166248466
37	ZNF143	chr4:166248212-166249068	K562	blood:	n/a	n/a
38	TBP	chr4:166248060-166249435	K562	blood:	n/a	n/a
39	POLR2A	chr4:166248003-166249207	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr4:166247984-166249168	H1-hESC	embryonic stem cell:	n/a	n/a
41	CUX1	chr4:166247860-166248293	GM12878	blood:	n/a	n/a
42	MYBL2	chr4:166248124-166249392	HepG2	liver:	n/a	n/a
43	POLR2A	chr4:166247960-166249421	GM18951	blood:	n/a	n/a
44	NFATC1	chr4:166248001-166248663	GM12878	blood:	n/a	n/a
45	POLR2A	chr4:166248121-166249400	GM12878	blood:	n/a	n/a
46	SIN3A	chr4:166247613-166250336	H1-hESC	embryonic stem cell:	n/a	chr4:166248619-166248633 chr4:166248448-166248461
47	TEAD4	chr4:166248032-166248652	K562	blood:	n/a	n/a
48	CCNT2	chr4:166248147-166249431	K562	blood:	n/a	n/a
49	POLR2A	chr4:166247716-166249507	HCT-116	colon:	n/a	n/a
50	MBD4	chr4:166247977-166248517	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:166033254..166035775-chr4:166247057..166248909,2	MCF-7	breast:
2	chr4:166127386..166130072-chr4:166247171..166250406,6	MCF-7	breast:
3	chr4:166127276..166130366-chr4:166247405..166250443,3	K562	blood:
4	chr4:166033415..166035712-chr4:166248207..166249791,2	MCF-7	breast:
5	chr4:166128531..166130929-chr4:166246215..166249595,5	MCF-7	breast:
6	chr4:166126308..166130366-chr4:166247405..166251145,5	K562	blood:

Variant related genes	Relation type
MSMO1	TF binding region
ENSG00000170088	Chromatin interaction
ENSG00000109466	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv3422247	chr4:166247552-166250050	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166247000-166251600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:166247200-166248400	Weak transcription	Lung	lung
3	chr4:166247400-166250400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:166247600-166248400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr4:166247600-166249200	Active TSS	Rectal Smooth Muscle	rectum
6	chr4:166247600-166249200	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr4:166247600-166249200	Active TSS	Stomach Smooth Muscle	stomach
8	chr4:166247600-166249600	Active TSS	Thymus	Thymus
9	chr4:166247600-166249800	Active TSS	A549	lung
10	chr4:166247600-166250000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:166247600-166250400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr4:166247600-166250400	Active TSS	Brain Substantia Nigra	brain
13	chr4:166247600-166250400	Active TSS	Right Atrium	heart
14	chr4:166247600-166251400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:166247600-166251600	Active TSS	H9 Cell Line	embryonic stem cell
16	chr4:166247600-166251800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:166247800-166248400	Weak transcription	Spleen	Spleen
18	chr4:166247800-166248800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:166247800-166248800	Active TSS	Brain Germinal Matrix	brain
20	chr4:166247800-166249000	Active TSS	Fetal Brain Female	brain
21	chr4:166247800-166249000	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:166247800-166249000	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr4:166247800-166249200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:166247800-166249200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:166247800-166249200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr4:166247800-166249200	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr4:166247800-166249200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:166247800-166249200	Active TSS	Brain Angular Gyrus	brain
29	chr4:166247800-166249200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:166247800-166249200	Active TSS	Fetal Kidney	kidney
31	chr4:166247800-166249200	Active TSS	Fetal Lung	lung
32	chr4:166247800-166249200	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:166247800-166249200	Active TSS	Right Ventricle	heart
34	chr4:166247800-166249400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:166247800-166249400	Active TSS	Brain Anterior Caudate	brain
36	chr4:166247800-166249400	Active TSS	Brain Cingulate Gyrus	brain
37	chr4:166247800-166249400	Active TSS	Colon Smooth Muscle	Colon
38	chr4:166247800-166249400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr4:166247800-166249400	Active TSS	Fetal Stomach	stomach
40	chr4:166247800-166249600	Active TSS	Brain Hippocampus Middle	brain
41	chr4:166247800-166249600	ZNF genes & repeats	Fetal Brain Male	brain
42	chr4:166247800-166249800	Active TSS	Liver	Liver
43	chr4:166247800-166249800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr4:166247800-166250000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:166247800-166250000	Active TSS	Psoas Muscle	Psoas
46	chr4:166247800-166250200	Active TSS	Duodenum Mucosa	Duodenum
47	chr4:166247800-166250200	Active TSS	K562	blood
48	chr4:166247800-166250400	Active TSS	Aorta	Aorta
49	chr4:166247800-166250400	Active TSS	Fetal Muscle Trunk	muscle
50	chr4:166247800-166250400	Active TSS	Ovary	ovary

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