Variant report

Variant	rs1528879
Chromosome Location	chr10:54073752-54073753
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	MAZ	chr10:54073306-54074631	HepG2	liver:	n/a	n/a
2	MAX	chr10:54073032-54075312	A549	lung:	n/a	n/a
3	POLR2A	chr10:54072994-54075187	MCF-7	breast:	n/a	n/a
4	RXRA	chr10:54073541-54074702	SK-N-SH	brain:	n/a	chr10:54074160-54074169
5	RFX5	chr10:54073484-54074380	HepG2	liver:	n/a	n/a
6	RXRA	chr10:54073722-54074117	HepG2	liver:	n/a	n/a
7	TCF7L2	chr10:54073629-54074374	HepG2	liver:	n/a	chr10:54073942-54073956
8	CREB1	chr10:54073666-54074925	HepG2	liver:	n/a	n/a
9	POLR2A	chr10:54073615-54076920	HUVEC	blood vessel:	n/a	n/a
10	TAF1	chr10:54073728-54074236	SK-N-SH	brain:	n/a	n/a
11	MAZ	chr10:54073295-54075277	IMR90	lung:	n/a	n/a
12	MAFK	chr10:54073545-54073892	HepG2	liver:	n/a	n/a
13	PBX3	chr10:54073599-54074990	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr10:54073700-54074726	HCT-116	colon:	n/a	chr10:54073933-54073946
15	REST	chr10:54072922-54075349	A549	lung:	n/a	chr10:54073933-54073946
16	CEBPB	chr10:54073328-54074677	A549	lung:	n/a	n/a
17	POLR2A	chr10:54073649-54074878	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr10:54072977-54075692	Gliobla	brain:	n/a	n/a
19	TBP	chr10:54073663-54074411	Hela-S3	cervix:	n/a	n/a
20	MAFK	chr10:54073465-54073816	HepG2	liver:	n/a	n/a
21	SP1	chr10:54073169-54075305	A549	lung:	n/a	chr10:54074927-54074937 chr10:54074910-54074919 chr10:54074913-54074927 chr10:54074927-54074936 chr10:54074926-54074938 chr10:54074905-54074914 chr10:54074909-54074921 chr10:54074923-54074937 chr10:54074911-54074920 chr10:54074926-54074938 chr10:54074910-54074920 chr10:54074909-54074921
22	EP300	chr10:54073705-54074156	SK-N-SH_RA	brain:	n/a	n/a
23	ARID3A	chr10:54072857-54074523	HepG2	liver:	n/a	n/a
24	EP300	chr10:54073707-54074161	SK-N-SH_RA	brain:	n/a	n/a
25	ZBTB7A	chr10:54073693-54074319	ECC-1	luminal epithelium:	n/a	n/a
26	REST	chr10:54073522-54074886	A549	lung:	n/a	chr10:54073933-54073946
27	CHD2	chr10:54073667-54074654	Hela-S3	cervix:	n/a	n/a
28	RFX5	chr10:54073572-54074820	Hela-S3	cervix:	n/a	n/a
29	GATA3	chr10:54072994-54074515	MCF-7	breast:	n/a	n/a
30	TAF1	chr10:54073693-54074415	MCF-7	breast:	n/a	n/a
31	NR3C1	chr10:54073689-54074162	A549	lung:	n/a	n/a
32	CEBPD	chr10:54073575-54074411	HepG2	liver:	n/a	n/a
33	POLR2A	chr10:54073653-54075058	MCF-7	breast:	n/a	n/a
34	POLR2A	chr10:54073685-54075047	A549	lung:	n/a	n/a
35	CEBPB	chr10:54073697-54074786	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr10:54073652-54074357	H1-neurons	neurons:	n/a	n/a
37	YY1	chr10:54073682-54074458	HepG2	liver:	n/a	n/a
38	JUND	chr10:54073611-54075480	A549	lung:	n/a	n/a
39	POLR2A	chr10:54073464-54075557	HUVEC	blood vessel:	n/a	n/a
40	MAFK	chr10:54073480-54073799	IMR90	lung:	n/a	n/a
41	ELF1	chr10:54073749-54074288	A549	lung:	n/a	chr10:54074030-54074042
42	REST	chr10:54073751-54074447	SK-N-SH	brain:	n/a	chr10:54073933-54073946
43	TEAD4	chr10:54073646-54074334	HepG2	liver:	n/a	n/a
44	FOXM1	chr10:54073739-54074540	ECC-1	luminal epithelium:	n/a	n/a
45	EP300	chr10:54073486-54074630	HepG2	liver:	n/a	chr10:54074160-54074174
46	NR2F2	chr10:54073540-54074356	MCF-7	breast:	n/a	n/a
47	GATA2	chr10:54072878-54074785	SH-SY5Y	brain:	n/a	n/a
48	CHD2	chr10:54073312-54074500	H1-hESC	embryonic stem cell:	n/a	n/a
49	SIN3AK20	chr10:54073685-54074907	SK-N-SH	brain:	n/a	n/a
50	RAD21	chr10:54073545-54074613	Hela-S3	cervix:	n/a	chr10:54074080-54074090 chr10:54074078-54074091

No.	Distal block	Cell Line	Cell type
1	chr10:54065577..54083492-chr10:54193846..54218961,120	MCF-7	breast:
2	chr10:54073525..54075924-chr10:54146848..54149629,2	MCF-7	breast:
3	chr10:54073396..54076476-chr10:54227833..54231095,3	MCF-7	breast:
4	chr10:54073032..54076598-chr10:54229475..54234592,10	MCF-7	breast:
5	chr10:54071324..54082180-chr10:54192987..54217560,81	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MBL2-5	chr10:54073394-54073888	ENSG00000236671
2	lnc-MBL2-5	chr10:54073394-54073870	NONHSAT013418
3	lnc-MBL2-5	chr10:54073394-54073888	NR_038277

Variant related genes	Relation type
DKK1	TF binding region
ENSG00000213657	Chromatin interaction
ENSG00000231131	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1528878	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59544809	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7069912	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045692	chr10:53301450-54086823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv532194	chr10:53746620-54735550	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv895399	chr10:53900872-54219820	Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv895400	chr10:54073294-54094359	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54068800-54073800	Weak transcription	Lung	lung
2	chr10:54072600-54075000	Active TSS	A549	lung
3	chr10:54072800-54073800	Bivalent Enhancer	Liver	Liver
4	chr10:54072800-54073800	Flanking Active TSS	Brain Angular Gyrus	brain
5	chr10:54072800-54073800	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr10:54072800-54073800	Active TSS	Right Ventricle	heart
7	chr10:54072800-54073800	Flanking Active TSS	NHEK	skin
8	chr10:54072800-54074400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr10:54072800-54074400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr10:54072800-54074400	Active TSS	Right Atrium	heart
11	chr10:54072800-54074800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
12	chr10:54072800-54074800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr10:54072800-54075200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr10:54072800-54075200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:54072800-54075800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:54072800-54075800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:54073000-54073800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:54073000-54073800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:54073000-54073800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
20	chr10:54073000-54073800	Enhancers	Gastric	stomach
21	chr10:54073000-54073800	Flanking Active TSS	Osteobl	bone
22	chr10:54073000-54074200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
23	chr10:54073000-54074200	Flanking Bivalent TSS/Enh	Placenta	Placenta
24	chr10:54073000-54074400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr10:54073000-54074800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:54073000-54074800	Bivalent/Poised TSS	Aorta	Aorta
28	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
31	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
32	chr10:54073000-54074800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
33	chr10:54073000-54074800	Enhancers	Spleen	Spleen
34	chr10:54073000-54075000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
35	chr10:54073000-54075800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:54073200-54073800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:54073200-54073800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
38	chr10:54073200-54073800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
39	chr10:54073200-54073800	Flanking Active TSS	Hela-S3	cervix
40	chr10:54073200-54074000	Active TSS	Esophagus	oesophagus
41	chr10:54073200-54074200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
42	chr10:54073200-54074400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr10:54073200-54074400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:54073200-54074400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr10:54073200-54074400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
46	chr10:54073200-54074400	Active TSS	Fetal Kidney	kidney
47	chr10:54073200-54074400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr10:54073200-54074600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr10:54073200-54074800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
50	chr10:54073200-54074800	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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