Variant report

Variant	rs72990460
Chromosome Location	chr1:114352418-114352419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr1:114352304-114352641	GM12878	blood:	n/a	n/a
2	CHD1	chr1:114352193-114352578	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:114352252-114352717	GM12878	blood:	n/a	n/a
4	SPI1	chr1:114352325-114352620	GM12891	blood:	n/a	n/a
5	ARID3A	chr1:114351803-114353222	K562	blood:	n/a	n/a
6	EP300	chr1:114352191-114352502	GM12878	blood:	n/a	n/a
7	SPI1	chr1:114352410-114352504	GM12878	blood:	n/a	n/a
8	NR2F2	chr1:114352322-114352998	MCF-7	breast:	n/a	n/a
9	SPI1	chr1:114352288-114352703	GM12891	blood:	n/a	n/a
10	GATA3	chr1:114352307-114352931	MCF-7	breast:	n/a	chr1:114352758-114352768 chr1:114352314-114352324
11	JUN	chr1:114352049-114356471	K562	blood:	n/a	n/a
12	FOXA1	chr1:114352395-114353024	HepG2	liver:	n/a	n/a
13	RCOR1	chr1:114352417-114352887	K562	blood:	n/a	n/a
14	FOXA2	chr1:114352323-114353264	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114327966..114331682-chr1:114351317..114354646,4	K562	blood:
2	chr1:114351776..114354778-chr1:114417690..114420488,3	MCF-7	breast:
3	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
4	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
5	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
6	chr1:114299192..114304079-chr1:114351100..114353758,4	K562	blood:
7	chr1:108135408..108137327-chr1:114351210..114352891,3	MCF-7	breast:
8	chr1:108269564..108272129-chr1:114352003..114353705,2	MCF-7	breast:
9	chr1:114349816..114352777-chr1:115298832..115300694,3	MCF-7	breast:
10	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
11	chr1:114300040..114303354-chr1:114351974..114356702,9	MCF-7	breast:
12	chr1:114300710..114302540-chr1:114351249..114353221,2	K562	blood:
13	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
14	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:
15	chr1:114351754..114354517-chr1:115321851..115324314,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231128	TF binding region
ENSG00000009307	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000052723	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000235527	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs60565055	1.00[AMR][1000 genomes]
rs72986647	1.00[AMR][1000 genomes]
rs72988553	1.00[AMR][1000 genomes]
rs72988578	1.00[AMR][1000 genomes]
rs72988587	1.00[AMR][1000 genomes]
rs72990447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72990454	1.00[AMR][1000 genomes]
rs72998111	1.00[AMR][1000 genomes]
rs72998179	1.00[AMR][1000 genomes]
rs72998192	1.00[AMR][1000 genomes]
rs73000165	1.00[AMR][1000 genomes]
rs73000167	1.00[AMR][1000 genomes]
rs73000171	1.00[AMR][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:114329200-114353600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:114332400-114353400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:114337200-114352600	Weak transcription	Fetal Kidney	kidney
8	chr1:114340400-114352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:114340600-114353400	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:114340800-114352600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:114340800-114352800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:114342000-114352600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:114347000-114352600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:114347400-114352600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:114347400-114352600	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:114348000-114352600	Weak transcription	HSMM	muscle
17	chr1:114348200-114353600	Weak transcription	Placenta	Placenta
18	chr1:114348600-114352600	Weak transcription	Small Intestine	intestine
19	chr1:114348600-114353800	Weak transcription	Gastric	stomach
20	chr1:114349800-114352600	Weak transcription	Left Ventricle	heart
21	chr1:114349800-114353600	Weak transcription	Lung	lung
22	chr1:114350000-114352600	Weak transcription	Fetal Stomach	stomach
23	chr1:114350400-114352800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:114350600-114352600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:114350600-114352600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:114350600-114352600	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:114350600-114352600	Enhancers	Colon Smooth Muscle	Colon
28	chr1:114350600-114353000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:114350800-114353400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:114351000-114352600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:114351000-114352600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr1:114351000-114353600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:114351200-114352600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:114351200-114352600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:114351200-114352600	Enhancers	Liver	Liver
36	chr1:114351200-114352600	Enhancers	Brain Angular Gyrus	brain
37	chr1:114351200-114352600	Enhancers	Brain Anterior Caudate	brain
38	chr1:114351200-114352800	Enhancers	Adipose Nuclei	Adipose
39	chr1:114351200-114352800	Enhancers	Fetal Intestine Small	intestine
40	chr1:114351400-114352600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:114351400-114352600	Active TSS	Aorta	Aorta
42	chr1:114351400-114352600	Enhancers	Right Ventricle	heart
43	chr1:114351400-114352800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr1:114351400-114353000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:114351400-114353400	Enhancers	Brain Substantia Nigra	brain
46	chr1:114351400-114354000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:114351600-114352600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:114351600-114352600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr1:114351600-114352600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr1:114351600-114352800	Flanking Active TSS	K562	blood

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