Variant report

Variant	rs2688245
Chromosome Location	chr4:8437635-8437636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr4:8437266-8437905	K562	blood:	n/a	chr4:8437442-8437463
2	POLR2A	chr4:8437502-8437875	GM12891	blood:	n/a	n/a
3	TBP	chr4:8437447-8437920	GM12878	blood:	n/a	n/a
4	RUNX3	chr4:8437394-8437781	GM12878	blood:	n/a	n/a
5	SIN3A	chr4:8437624-8437824	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:8437544-8437902	GM12878	blood:	n/a	n/a
7	CTCF	chr4:8437600-8437750	GM12872	blood:	n/a	n/a
8	POLR2A	chr4:8437482-8438104	GM12891	blood:	n/a	n/a
9	POLR2A	chr4:8437439-8438082	GM19099	blood:	n/a	n/a
10	POLR2A	chr4:8437433-8437767	K562	blood:	n/a	n/a
11	SPI1	chr4:8437565-8437735	K562	blood:	n/a	n/a
12	POLR2A	chr4:8437368-8438069	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:8437509-8437927	GM12891	blood:	n/a	n/a
14	ZC3H11A	chr4:8437603-8437695	K562	blood:	n/a	n/a
15	MAX	chr4:8437481-8437710	K562	blood:	n/a	n/a
16	POLR2A	chr4:8437511-8438042	GM12878	blood:	n/a	n/a
17	MAZ	chr4:8437385-8437973	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:8437444-8438063	GM18951	blood:	n/a	n/a
19	POU2F2	chr4:8437430-8438095	GM12891	blood:	n/a	n/a
20	ZBTB7A	chr4:8437503-8437705	K562	blood:	n/a	n/a
21	CTCF	chr4:8437580-8437730	HPAF	blood vessel:	n/a	n/a
22	MTA3	chr4:8437431-8438004	GM12878	blood:	n/a	n/a
23	CTCF	chr4:8437520-8437670	GM12867	blood:	n/a	n/a
24	IKZF1	chr4:8437453-8437960	GM12878	blood:	n/a	n/a
25	NFIC	chr4:8437290-8437839	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:8437386-8437923	GM12892	blood:	n/a	n/a
27	MAX	chr4:8437442-8437989	GM12878	blood:	n/a	n/a
28	PBX3	chr4:8437618-8437824	GM12878	blood:	n/a	n/a
29	SMC3	chr4:8437561-8437686	GM12878	blood:	n/a	n/a
30	POU2F2	chr4:8437387-8438014	GM12891	blood:	n/a	n/a
31	MAZ	chr4:8437485-8437714	K562	blood:	n/a	n/a
32	UBTF	chr4:8437505-8437779	K562	blood:	n/a	n/a
33	SPI1	chr4:8437586-8437796	K562	blood:	n/a	n/a
34	CUX1	chr4:8437371-8438015	GM12878	blood:	n/a	n/a
35	SPI1	chr4:8437416-8438028	GM12878	blood:	n/a	n/a
36	TAL1	chr4:8437433-8437796	K562	blood:	n/a	n/a
37	MYC	chr4:8437606-8437831	K562	blood:	n/a	n/a
38	GATA2	chr4:8437368-8437766	K562	blood:	n/a	n/a
39	CHD1	chr4:8437200-8437695	GM12878	blood:	n/a	n/a
40	POU2F2	chr4:8437507-8437812	GM12878	blood:	n/a	n/a
41	TEAD4	chr4:8437364-8437786	K562	blood:	n/a	n/a
42	EP300	chr4:8437513-8437656	GM12878	blood:	n/a	n/a
43	GATA1	chr4:8437346-8438090	PBDE	blood:	n/a	n/a
44	POLR2A	chr4:8437466-8437821	K562	blood:	n/a	n/a
45	POU2F2	chr4:8437352-8438142	GM12878	blood:	n/a	n/a
46	SPI1	chr4:8437458-8437853	GM12891	blood:	n/a	n/a
47	CHD2	chr4:8437443-8437783	GM12878	blood:	n/a	n/a
48	HDAC2	chr4:8437460-8437705	K562	blood:	n/a	n/a
49	POLR2A	chr4:8437380-8438122	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:8437544-8437774	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8429518..8431924-chr4:8437588..8440150,2	MCF-7	breast:
2	chr4:8217481..8219669-chr4:8436164..8438381,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000087008	Chromatin interaction
ENSG00000125089	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10938711	1.00[AMR][1000 genomes]
rs1815073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2386226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3103096	0.90[AFR][1000 genomes]
rs3107679	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8430800-8439000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:8430800-8439000	Weak transcription	Brain Germinal Matrix	brain
3	chr4:8430800-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:8430800-8441400	Weak transcription	Fetal Brain Female	brain
5	chr4:8430800-8441800	Weak transcription	Aorta	Aorta
6	chr4:8431000-8439000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:8431000-8439000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:8431000-8439200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:8431000-8439200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:8431000-8439200	Weak transcription	Fetal Brain Male	brain
11	chr4:8431000-8440600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:8431000-8441000	Weak transcription	A549	lung
13	chr4:8431000-8441200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:8431000-8441600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:8433400-8439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:8433800-8442000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:8435600-8441200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:8435800-8438200	Enhancers	Stomach Mucosa	stomach
19	chr4:8436000-8438000	Active TSS	Ovary	ovary
20	chr4:8436000-8438200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr4:8436200-8438000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:8436200-8438200	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr4:8436400-8437800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:8436400-8439000	Weak transcription	Lung	lung
25	chr4:8436600-8438000	Active TSS	GM12878-XiMat	blood
26	chr4:8436800-8438200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:8437200-8437800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:8437200-8437800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:8437200-8437800	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr4:8437200-8437800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr4:8437200-8437800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr4:8437200-8437800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:8437200-8437800	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr4:8437200-8437800	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:8437200-8437800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:8437200-8437800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr4:8437200-8437800	Flanking Active TSS	Liver	Liver
38	chr4:8437200-8437800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr4:8437200-8437800	Active TSS	Fetal Intestine Large	intestine
40	chr4:8437200-8437800	Active TSS	Fetal Intestine Small	intestine
41	chr4:8437200-8437800	Active TSS	HSMM	muscle
42	chr4:8437200-8438000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr4:8437200-8438000	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr4:8437200-8438000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr4:8437200-8438000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:8437200-8438000	Active TSS	Colon Smooth Muscle	Colon
47	chr4:8437200-8438000	Enhancers	Fetal Muscle Leg	muscle
48	chr4:8437200-8438000	Flanking Active TSS	Fetal Thymus	thymus
49	chr4:8437200-8438000	Flanking Active TSS	NHEK	skin
50	chr4:8437200-8438200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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