Variant report

Variant	rs28744536
Chromosome Location	chr1:150537216-150537217
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	ZNF384	chr1:150536741-150537324	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:150533330-150537703	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:150536866-150537351	K562	blood:	n/a	n/a
6	POLR2A	chr1:150532058-150538177	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:150530539-150552850	MCF10A-Er-Src	breast:	n/a	n/a
8	RFX5	chr1:150532907-150537239	IMR90	lung:	n/a	chr1:150534721-150534730 chr1:150534717-150534732
9	EBF1	chr1:150537137-150537431	GM12878	blood:	n/a	chr1:150537323-150537334
10	RUNX3	chr1:150537136-150537502	GM12878	blood:	n/a	n/a
11	EBF1	chr1:150537192-150537417	GM12878	blood:	n/a	chr1:150537323-150537334
12	BHLHE40	chr1:150537211-150537628	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:150531141-150552175	A549	lung:	n/a	n/a
14	POLR2A	chr1:150529470-150537724	K562	blood:	n/a	n/a
15	RELA	chr1:150536960-150537506	GM19099	blood:	n/a	n/a
16	EBF1	chr1:150537136-150537589	GM12878	blood:	n/a	chr1:150537323-150537334
17	POLR2A	chr1:150527768-150537708	K562	blood:	n/a	n/a
18	POLR2A	chr1:150533277-150537531	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150488041..150489716-chr1:150536057..150538087,2	MCF-7	breast:
2	chr1:150449166..150451337-chr1:150534511..150537297,2	MCF-7	breast:
3	chr1:150336838..150338667-chr1:150536131..150537830,2	MCF-7	breast:
4	chr1:150531290..150540028-chr1:150591374..150603951,29	MCF-7	breast:
5	chr1:150536175..150539015-chr1:151037065..151039505,2	K562	blood:
6	chr1:150532182..150537720-chr1:150588719..150604935,28	MCF-7	breast:

Variant related genes	Relation type
ADAMTSL4-AS1	TF binding region
ENSG00000163125	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000228126	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1053701	0.85[ASN][1000 genomes]
rs11204665	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585460	0.82[ASN][1000 genomes]
rs12034302	0.86[ASN][1000 genomes]
rs12036914	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042580	0.83[ASN][1000 genomes]
rs60060012	0.86[ASN][1000 genomes]
rs61820166	0.86[ASN][1000 genomes]
rs61820168	0.85[ASN][1000 genomes]
rs61820170	0.82[ASN][1000 genomes]
rs6587515	0.81[ASN][1000 genomes]
rs6672667	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7517	0.85[ASN][1000 genomes]
rs7543465	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases
4	nsv527379	chr1:150527354-150542128	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
5	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150533600-150537400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:150534400-150539200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:150534400-150547200	Weak transcription	Ovary	ovary
4	chr1:150534600-150537600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:150534600-150537600	Enhancers	NHLF	lung
6	chr1:150534600-150539200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:150534600-150540200	Enhancers	Pancreas	Pancrea
8	chr1:150534600-150542600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:150534600-150542600	Enhancers	Lung	lung
10	chr1:150534800-150538400	Flanking Active TSS	GM12878-XiMat	blood
11	chr1:150534800-150539800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:150534800-150540400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:150535000-150537400	Enhancers	Spleen	Spleen
14	chr1:150535000-150537600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr1:150535000-150537600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:150535000-150537600	Enhancers	HUVEC	blood vessel
17	chr1:150535000-150538400	Enhancers	HMEC	breast
18	chr1:150535000-150539800	Enhancers	Fetal Lung	lung
19	chr1:150535000-150540000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:150535000-150540200	Enhancers	Left Ventricle	heart
21	chr1:150535000-150542200	Enhancers	Placenta	Placenta
22	chr1:150535200-150537400	Enhancers	Brain Substantia Nigra	brain
23	chr1:150535200-150537600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:150535200-150538000	Enhancers	Colon Smooth Muscle	Colon
25	chr1:150535200-150539800	Enhancers	Fetal Muscle Trunk	muscle
26	chr1:150535200-150540000	Enhancers	Fetal Intestine Large	intestine
27	chr1:150535200-150540000	Enhancers	Psoas Muscle	Psoas
28	chr1:150535200-150540000	Enhancers	Right Atrium	heart
29	chr1:150535200-150541000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:150535200-150541800	Enhancers	Small Intestine	intestine
31	chr1:150535400-150537600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:150535400-150537600	Enhancers	NH-A	brain
33	chr1:150535400-150537600	Enhancers	NHDF-Ad	bronchial
34	chr1:150535400-150537800	Enhancers	Brain Hippocampus Middle	brain
35	chr1:150535400-150539000	Enhancers	Fetal Muscle Leg	muscle
36	chr1:150535400-150539600	Enhancers	Liver	Liver
37	chr1:150535400-150539800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:150535400-150540200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:150535400-150540400	Enhancers	Fetal Heart	heart
40	chr1:150535600-150537400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:150535600-150537600	Enhancers	Brain Anterior Caudate	brain
42	chr1:150535600-150537600	Enhancers	HSMM	muscle
43	chr1:150535600-150540200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr1:150535800-150537400	Enhancers	Right Ventricle	heart
45	chr1:150535800-150537600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:150535800-150538200	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:150535800-150538200	Enhancers	Osteobl	bone
48	chr1:150535800-150539800	Enhancers	HSMMtube	muscle
49	chr1:150536000-150538000	Enhancers	Thymus	Thymus
50	chr1:150536000-150540800	Enhancers	Stomach Mucosa	stomach

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