Variant report

Variant	rs13353696
Chromosome Location	chr4:82393862-82393863
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	MAX	chr4:82392307-82393947	ECC-1	luminal epithelium:	n/a	chr4:82393763-82393772 chr4:82393172-82393181 chr4:82392754-82392764
2	POLR2A	chr4:82392673-82393886	PBDE	blood:	n/a	n/a
3	RCOR1	chr4:82392104-82393913	IMR90	lung:	n/a	n/a
4	TEAD4	chr4:82392733-82393964	ECC-1	luminal epithelium:	n/a	n/a
5	MXI1	chr4:82392769-82393876	IMR90	lung:	n/a	chr4:82393761-82393776 chr4:82393763-82393778
6	EP300	chr4:82392564-82393919	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr4:82391429-82394854	Raji	blood:	n/a	n/a
8	MAX	chr4:82393524-82393865	H1-hESC	embryonic stem cell:	n/a	chr4:82393763-82393772
9	KAP1	chr4:82393202-82393925	U2OS	brain:	n/a	chr4:82393496-82393504
10	FOXM1	chr4:82392697-82394009	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr4:82392687-82393944	ECC-1	luminal epithelium:	n/a	n/a
12	NFIC	chr4:82392743-82393893	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:82392247..82394728-chr4:83351803..83353310,2	MCF-7	breast:

Variant related genes	Relation type
RASGEF1B	TF binding region
ENSG00000145293	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10018892	0.91[AMR][1000 genomes]
rs10019254	0.91[AMR][1000 genomes]
rs10440362	0.85[EUR][1000 genomes]
rs13353699	1.00[GIH][hapmap]
rs17558056	1.00[TSI][hapmap]
rs17558175	1.00[TSI][hapmap]
rs28393966	0.91[AMR][1000 genomes]
rs28408727	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28410139	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41470747	1.00[TSI][hapmap]
rs56934019	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57077180	0.81[AMR][1000 genomes]
rs60006878	0.81[AMR][1000 genomes]
rs6846142	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72884907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73829600	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7693787	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829986	chr4:82345163-82509860	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82390600-82394200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr4:82391400-82394000	Active TSS	Fetal Intestine Large	intestine
3	chr4:82391800-82394000	Active TSS	Right Atrium	heart
4	chr4:82393200-82394400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:82393200-82394400	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr4:82393400-82394000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr4:82393400-82394000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr4:82393400-82394000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:82393400-82394000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:82393400-82394000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr4:82393400-82394000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr4:82393400-82394000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:82393400-82394000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr4:82393400-82394000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:82393400-82394000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr4:82393400-82394000	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr4:82393400-82394000	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr4:82393400-82394000	Flanking Active TSS	Placenta	Placenta
19	chr4:82393400-82394000	Flanking Active TSS	Fetal Stomach	stomach
20	chr4:82393400-82394000	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr4:82393400-82394200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr4:82393400-82394200	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr4:82393400-82394200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr4:82393400-82394400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:82393400-82394400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr4:82393400-82394400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr4:82393400-82394600	Flanking Active TSS	Liver	Liver
28	chr4:82393400-82394600	Enhancers	Spleen	Spleen
29	chr4:82393600-82394000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:82393600-82394000	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr4:82393600-82394000	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr4:82393600-82394000	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr4:82393600-82394000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr4:82393600-82394000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:82393600-82394200	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr4:82393600-82394200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr4:82393600-82394200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr4:82393600-82394200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
39	chr4:82393600-82394600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:82393600-82394600	Weak transcription	Lung	lung
41	chr4:82393600-82394800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr4:82393800-82394000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:82393800-82394000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:82393800-82394000	Enhancers	Brain Hippocampus Middle	brain
45	chr4:82393800-82394000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr4:82393800-82394000	Weak transcription	Colonic Mucosa	Colon
47	chr4:82393800-82394000	Enhancers	Fetal Brain Female	brain
48	chr4:82393800-82394000	Active TSS	Fetal Kidney	kidney
49	chr4:82393800-82394000	Active TSS	Fetal Lung	lung
50	chr4:82393800-82394200	Enhancers	HUES48 Cell Line	embryonic stem cell

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