Variant report

Variant	rs28677890
Chromosome Location	chr5:115911250-115911251
allele	C/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	RUNX3	chr5:115910294-115911315	GM12878	blood:	n/a	n/a
2	FOS	chr5:115910987-115912085	MCF10A-Er-Src	breast:	n/a	n/a
3	TBP	chr5:115910295-115912307	H1-hESC	embryonic stem cell:	n/a	n/a
4	MTA3	chr5:115910330-115911850	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:115911135-115912558	H1-hESC	embryonic stem cell:	n/a	n/a
6	STAT3	chr5:115910481-115911468	GM12878	blood:	n/a	n/a
7	BHLHE40	chr5:115911151-115912351	GM12878	blood:	n/a	n/a
8	RAD21	chr5:115907512-115912646	SK-N-SH	brain:	n/a	chr5:115907841-115907850 chr5:115911934-115911953 chr5:115907716-115907735 chr5:115908547-115908561
9	MAZ	chr5:115911249-115913425	GM12878	blood:	n/a	chr5:115912792-115912807 chr5:115912793-115912802 chr5:115912792-115912805 chr5:115912794-115912804 chr5:115911492-115911502 chr5:115912794-115912803 chr5:115912792-115912805 chr5:115912794-115912803 chr5:115912793-115912804 chr5:115912792-115912805 chr5:115912790-115912805 chr5:115912792-115912805 chr5:115912793-115912804 chr5:115912793-115912803
10	ZNF384	chr5:115910371-115912136	GM12878	blood:	n/a	chr5:115911901-115911909
11	USF2	chr5:115911169-115912047	H1-hESC	embryonic stem cell:	n/a	n/a
12	EBF1	chr5:115910383-115913484	GM12878	blood:	n/a	chr5:115912875-115912886 chr5:115912878-115912887
13	TBP	chr5:115910339-115911480	GM12878	blood:	n/a	n/a
14	KAP1	chr5:115910420-115911889	HEK293	kidney:	n/a	n/a
15	CTCF	chr5:115911200-115911350	A549	lung:	n/a	n/a
16	MXI1	chr5:115906888-115912476	SK-N-SH	brain:	n/a	n/a
17	MYC	chr5:115911133-115912022	MCF10A-Er-Src	breast:	n/a	chr5:115911492-115911502
18	CTCF	chr5:115911200-115911350	GM12864	blood:	n/a	n/a
19	MYC	chr5:115911131-115912029	H1-hESC	embryonic stem cell:	n/a	chr5:115911492-115911502
20	POLR2A	chr5:115910283-115913382	GM12878	blood:	n/a	n/a
21	MYC	chr5:115910365-115912047	MCF10A-Er-Src	breast:	n/a	chr5:115911492-115911502
22	POLR2A	chr5:115911178-115912485	GM12878	blood:	n/a	n/a
23	CHD1	chr5:115910361-115913446	GM12878	blood:	n/a	n/a
24	MXI1	chr5:115908940-115912224	GM12878	blood:	n/a	n/a
25	GATA3	chr5:115910848-115911291	SH-SY5Y	brain:	n/a	chr5:115911125-115911135 chr5:115911125-115911132 chr5:115911125-115911132 chr5:115911125-115911132 chr5:115911123-115911133
26	CTCF	chr5:115910310-115912531	GM12878	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
27	TAF7	chr5:115911210-115912294	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr5:115910307-115912244	MCF10A-Er-Src	breast:	n/a	n/a
29	SMC3	chr5:115907633-115912597	SK-N-SH	brain:	n/a	chr5:115908994-115909004 chr5:115907717-115907731 chr5:115911939-115911949 chr5:115909229-115909236
30	SMC3	chr5:115910369-115913364	GM12878	blood:	n/a	chr5:115911939-115911949
31	POLR2A	chr5:115911190-115912286	H1-hESC	embryonic stem cell:	n/a	n/a
32	CHD1	chr5:115908188-115911902	H1-hESC	embryonic stem cell:	n/a	chr5:115910287-115910297
33	POLR2A	chr5:115909767-115912046	MCF10A-Er-Src	breast:	n/a	n/a
34	SIN3A	chr5:115907561-115912449	H1-hESC	embryonic stem cell:	n/a	chr5:115910340-115910351 chr5:115908696-115908709 chr5:115909519-115909530
35	EP300	chr5:115910334-115911455	GM12878	blood:	n/a	chr5:115910855-115910869 chr5:115910340-115910356 chr5:115910536-115910552 chr5:115910535-115910551 chr5:115910849-115910863 chr5:115910851-115910865 chr5:115910854-115910868
36	POLR2A	chr5:115911157-115911504	GM12878	blood:	n/a	n/a
37	TBL1XR1	chr5:115911155-115913346	GM12878	blood:	n/a	n/a
38	CTCF	chr5:115911027-115912516	SK-N-SH	brain:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
39	FOS	chr5:115911036-115911545	MCF10A-Er-Src	breast:	n/a	n/a
40	YY1	chr5:115911225-115911551	H1-hESC	embryonic stem cell:	n/a	n/a
41	CHD2	chr5:115911205-115912448	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115904366..115906105-chr5:115910810..115912566,2	K562	blood:

Variant related genes	Relation type
SEMA6A	TF binding region

rs_ID	r²[population]
rs10037569	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10061468	1.00[EUR][1000 genomes]
rs10073342	1.00[EUR][1000 genomes]
rs12332586	1.00[EUR][1000 genomes]
rs13355107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13355323	1.00[EUR][1000 genomes]
rs13362514	1.00[EUR][1000 genomes]
rs17140058	1.00[EUR][1000 genomes]
rs17140180	1.00[EUR][1000 genomes]
rs4379240	1.00[EUR][1000 genomes]
rs58841498	1.00[EUR][1000 genomes]
rs60190258	1.00[EUR][1000 genomes]
rs640121	1.00[EUR][1000 genomes]
rs6864548	1.00[EUR][1000 genomes]
rs6897908	1.00[EUR][1000 genomes]
rs73256769	1.00[EUR][1000 genomes]
rs73780329	1.00[EUR][1000 genomes]
rs73780382	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7711834	1.00[EUR][1000 genomes]
rs7718743	1.00[EUR][1000 genomes]

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115906000-115912400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:115906400-115912200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr5:115906400-115912400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:115906800-115912600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:115906800-115912800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:115907000-115912200	Active TSS	Fetal Intestine Large	intestine
7	chr5:115907000-115912400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:115907200-115912200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:115907200-115912600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:115907200-115912600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:115907400-115911400	Active TSS	Colon Smooth Muscle	Colon
12	chr5:115907400-115911400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr5:115907400-115912200	Active TSS	Fetal Intestine Small	intestine
14	chr5:115907400-115912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr5:115907400-115912600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:115907400-115912600	Active TSS	Brain Angular Gyrus	brain
17	chr5:115907600-115912000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr5:115907600-115912400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:115907600-115912400	Active TSS	Ovary	ovary
20	chr5:115907600-115912600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:115907600-115912600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:115907600-115912600	Active TSS	Brain Anterior Caudate	brain
23	chr5:115907600-115912600	Active TSS	Brain Cingulate Gyrus	brain
24	chr5:115907600-115912600	Active TSS	Brain Substantia Nigra	brain
25	chr5:115907800-115912600	Active TSS	Fetal Kidney	kidney
26	chr5:115908000-115912400	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr5:115908000-115912400	Bivalent/Poised TSS	Thymus	Thymus
28	chr5:115908000-115912600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:115908200-115912400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr5:115908200-115912400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:115908200-115912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr5:115908400-115912000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
33	chr5:115908400-115912400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr5:115908400-115912400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:115908400-115912600	Active TSS	H9 Cell Line	embryonic stem cell
36	chr5:115908600-115911400	Active TSS	Left Ventricle	heart
37	chr5:115908600-115911600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
38	chr5:115908600-115911800	Active TSS	Aorta	Aorta
39	chr5:115909000-115911400	Active TSS	Brain Hippocampus Middle	brain
40	chr5:115909000-115912400	Active TSS	Stomach Smooth Muscle	stomach
41	chr5:115909200-115911600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:115909200-115912600	Active TSS	Right Atrium	heart
43	chr5:115909400-115912000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr5:115909400-115912800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr5:115909600-115911400	Active TSS	Placenta	Placenta
46	chr5:115909600-115911600	Active TSS	HSMMtube	muscle
47	chr5:115909600-115912200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:115909600-115912400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr5:115909600-115912400	Active TSS	Rectal Smooth Muscle	rectum
50	chr5:115909600-115912400	Active TSS	Small Intestine	intestine

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