Variant report

Variant	rs2389871
Chromosome Location	chr4:120550639-120550640
allele	A/T
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	POLR2A	chr4:120547582-120550654	PANC-1	pancreas:	n/a	n/a
2	MAZ	chr4:120548187-120550732	IMR90	lung:	n/a	chr4:120550032-120550042 chr4:120550059-120550069
3	CTCF	chr4:120548079-120550795	SK-N-SH	brain:	n/a	chr4:120548991-120549004 chr4:120550066-120550075
4	ZBTB7A	chr4:120549618-120550655	ECC-1	luminal epithelium:	n/a	n/a
5	RAD21	chr4:120548295-120550823	IMR90	lung:	n/a	chr4:120550041-120550055 chr4:120549350-120549359 chr4:120548632-120548646 chr4:120548656-120548669 chr4:120548955-120548968
6	CTCF	chr4:120550500-120550650	HVMF	connective:	n/a	n/a
7	RAD21	chr4:120549860-120550691	HCT-116	colon:	n/a	chr4:120550041-120550055
8	MAX	chr4:120549462-120550670	ECC-1	luminal epithelium:	n/a	chr4:120550032-120550042 chr4:120550059-120550069
9	CHD1	chr4:120545491-120550997	IMR90	lung:	n/a	chr4:120549245-120549255
10	HA-E2F1	chr4:120548111-120550675	MCF-7	breast:	n/a	chr4:120550181-120550191 chr4:120548252-120548261 chr4:120550036-120550046 chr4:120549057-120549064 chr4:120548994-120549004 chr4:120548902-120548914
11	SMC3	chr4:120547429-120550809	SK-N-SH	brain:	n/a	chr4:120548994-120549004
12	RAD21	chr4:120549783-120550653	HCT-116	colon:	n/a	chr4:120550041-120550055
13	RAD21	chr4:120548128-120551034	SK-N-SH	brain:	n/a	chr4:120550041-120550055 chr4:120549350-120549359 chr4:120548632-120548646 chr4:120548656-120548669 chr4:120548955-120548968

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120550305..120551270-chr4:120977378..120978356,2	MCF-7	breast:
2	chr4:120550452..120551201-chr4:120970722..120971578,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC110373.1-9	chr4:120548945-120551908	NONHSAT098098

Variant related genes	Relation type
PDE5A	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10013852	0.84[AFR][1000 genomes]
rs10021469	0.84[AFR][1000 genomes]
rs13119104	1.00[YRI][hapmap]
rs13125819	1.00[YRI][hapmap]
rs17005698	0.92[YRI][hapmap]
rs2256645	0.92[YRI][hapmap]
rs2389865	0.83[YRI][hapmap]
rs2389872	0.92[AFR][1000 genomes]
rs2389876	1.00[AFR][1000 genomes]
rs2389877	1.00[AFR][1000 genomes]
rs2389878	1.00[AFR][1000 genomes]
rs2622497	0.91[YRI][hapmap]
rs2715020	0.92[YRI][hapmap]
rs2715021	0.83[YRI][hapmap]
rs2928991	1.00[YRI][hapmap]
rs2953290	0.96[AFR][1000 genomes]
rs2953292	0.92[YRI][hapmap]
rs2953294	0.92[AFR][1000 genomes]
rs3109370	0.81[AFR][1000 genomes]
rs4146266	1.00[YRI][hapmap]
rs4264816	0.92[YRI][hapmap]
rs4833621	0.88[AFR][1000 genomes]
rs6534145	0.84[AFR][1000 genomes]
rs6534148	0.88[AFR][1000 genomes]
rs6831062	0.88[AFR][1000 genomes]
rs6845402	0.91[YRI][hapmap]
rs6854072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7665086	0.83[YRI][hapmap]
rs9307480	0.84[AFR][1000 genomes];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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120544800-120550800	Active TSS	Stomach Smooth Muscle	stomach
2	chr4:120546600-120550800	Active TSS	Right Atrium	heart
3	chr4:120546600-120551000	Active TSS	NHLF	lung
4	chr4:120547400-120550800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr4:120547400-120550800	Active TSS	NHDF-Ad	bronchial
6	chr4:120547800-120550800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr4:120548000-120550800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:120548000-120550800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:120548000-120550800	Bivalent/Poised TSS	Fetal Brain Female	brain
10	chr4:120548000-120551000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:120548000-120551000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:120548200-120550800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:120548200-120550800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:120548400-120550800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr4:120548600-120550800	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr4:120549400-120550800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:120549800-120550800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr4:120550200-120550800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
19	chr4:120550200-120550800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr4:120550200-120550800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:120550200-120550800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
22	chr4:120550200-120550800	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr4:120550200-120550800	Enhancers	Fetal Heart	heart
24	chr4:120550200-120550800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr4:120550200-120550800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr4:120550200-120550800	Flanking Bivalent TSS/Enh	Thymus	Thymus
27	chr4:120550400-120550800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:120550400-120550800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:120550400-120550800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr4:120550400-120550800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
31	chr4:120550400-120550800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:120550400-120550800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr4:120550400-120550800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:120550400-120550800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:120550400-120550800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:120550400-120550800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:120550400-120550800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:120550400-120550800	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr4:120550400-120550800	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr4:120550400-120550800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr4:120550400-120550800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:120550400-120550800	Flanking Active TSS	GM12878-XiMat	blood
43	chr4:120550400-120550800	Flanking Active TSS	NH-A	brain
44	chr4:120550400-120550800	Flanking Active TSS	NHEK	skin
45	chr4:120550400-120551000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr4:120550400-120551400	Flanking Active TSS	Osteobl	bone
47	chr4:120550600-120550800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:120550600-120550800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
49	chr4:120550600-120550800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:120550600-120550800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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