Variant report

Variant	rs6854072
Chromosome Location	chr4:120549435-120549436
allele	G/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	MAZ	chr4:120549105-120549444	GM12878	blood:	n/a	n/a
2	ZNF263	chr4:120548205-120550586	HEK293-T-REx	kidney:	n/a	chr4:120550414-120550423 chr4:120548899-120548908 chr4:120549247-120549256
3	POLR2A	chr4:120547582-120550654	PANC-1	pancreas:	n/a	n/a
4	MAZ	chr4:120548187-120550732	IMR90	lung:	n/a	chr4:120550032-120550042 chr4:120550059-120550069
5	YY1	chr4:120548953-120549484	H1-hESC	embryonic stem cell:	n/a	chr4:120549005-120549016 chr4:120548970-120548981
6	POLR2A	chr4:120548572-120550493	IMR90	lung:	n/a	n/a
7	TCF7L2	chr4:120548277-120550472	HCT-116	colon:	n/a	n/a
8	TAF1	chr4:120548812-120549437	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr4:120548079-120550795	SK-N-SH	brain:	n/a	chr4:120548991-120549004 chr4:120550066-120550075
10	POLR2A	chr4:120548122-120550446	PANC-1	pancreas:	n/a	n/a
11	CTBP2	chr4:120548261-120549529	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr4:120548295-120550823	IMR90	lung:	n/a	chr4:120550041-120550055 chr4:120549350-120549359 chr4:120548632-120548646 chr4:120548656-120548669 chr4:120548955-120548968
13	ZBTB7A	chr4:120548677-120549543	ECC-1	luminal epithelium:	n/a	chr4:120548699-120548706
14	MAZ	chr4:120549354-120549495	K562	blood:	n/a	n/a
15	CHD1	chr4:120545491-120550997	IMR90	lung:	n/a	chr4:120549245-120549255
16	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
17	SMC3	chr4:120547429-120550809	SK-N-SH	brain:	n/a	chr4:120548994-120549004
18	POLR2A	chr4:120548220-120550427	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZBTB7A	chr4:120548046-120549523	ECC-1	luminal epithelium:	n/a	chr4:120548699-120548706
20	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
21	TCF7L2	chr4:120549383-120549808	HEK293	kidney:	n/a	n/a
22	MXI1	chr4:120547464-120550626	IMR90	lung:	n/a	n/a
23	SIN3AK20	chr4:120548070-120550361	PANC-1	pancreas:	n/a	n/a
24	SIN3A	chr4:120548010-120550529	H1-hESC	embryonic stem cell:	n/a	chr4:120550042-120550055 chr4:120548634-120548643
25	CTCF	chr4:120549400-120549550	AoAF	blood vessel:	n/a	n/a
26	POLR2A	chr4:120548477-120550521	H1-hESC	embryonic stem cell:	n/a	n/a
27	REST	chr4:120549085-120549445	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120548759..120550296-chr4:120986622..120988750,2	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
ENSG00000250938	Chromatin interaction
ENSG00000164109	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10013852	0.88[AFR][1000 genomes]
rs10021469	0.88[AFR][1000 genomes]
rs13119104	0.82[AFR][1000 genomes]
rs13125819	0.82[AFR][1000 genomes]
rs2389871	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2389872	0.88[AFR][1000 genomes]
rs2389876	0.96[AFR][1000 genomes]
rs2389877	0.96[AFR][1000 genomes]
rs2389878	0.96[AFR][1000 genomes]
rs2389884	0.82[AFR][1000 genomes]
rs2928991	0.82[AFR][1000 genomes]
rs2953290	1.00[AFR][1000 genomes]
rs2953294	0.96[AFR][1000 genomes]
rs3109370	0.84[AFR][1000 genomes]
rs4146266	0.82[AFR][1000 genomes]
rs4833621	0.92[AFR][1000 genomes]
rs6534145	0.88[AFR][1000 genomes]
rs6534148	0.92[AFR][1000 genomes]
rs6831062	0.92[AFR][1000 genomes]
rs7439678	0.82[AFR][1000 genomes]
rs9307480	0.88[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120544400-120550600	Active TSS	Aorta	Aorta
2	chr4:120544800-120550800	Active TSS	Stomach Smooth Muscle	stomach
3	chr4:120545200-120550400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:120545200-120550600	Active TSS	Colon Smooth Muscle	Colon
5	chr4:120545600-120550600	Active TSS	Fetal Kidney	kidney
6	chr4:120545800-120550600	Active TSS	Rectal Smooth Muscle	rectum
7	chr4:120546000-120550600	Active TSS	Fetal Lung	lung
8	chr4:120546200-120550600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:120546400-120550400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:120546600-120550800	Active TSS	Right Atrium	heart
11	chr4:120546600-120551000	Active TSS	NHLF	lung
12	chr4:120547000-120550400	Active TSS	Osteobl	bone
13	chr4:120547200-120550600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr4:120547400-120550200	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr4:120547400-120550200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr4:120547400-120550600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:120547400-120550600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:120547400-120550800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr4:120547400-120550800	Active TSS	NHDF-Ad	bronchial
20	chr4:120547600-120549800	Active TSS	Colonic Mucosa	Colon
21	chr4:120547600-120550200	Active TSS	Esophagus	oesophagus
22	chr4:120547600-120550400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:120547600-120550400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:120547600-120550400	Active TSS	Brain Anterior Caudate	brain
25	chr4:120547600-120550400	Active TSS	Pancreas	Pancrea
26	chr4:120547600-120550600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr4:120547600-120550600	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr4:120547600-120550600	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr4:120547600-120550600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:120547600-120550600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:120547600-120550600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:120547600-120550600	Active TSS	Left Ventricle	heart
33	chr4:120547600-120550600	Active TSS	Psoas Muscle	Psoas
34	chr4:120547600-120550600	Active TSS	Right Ventricle	heart
35	chr4:120547800-120549800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr4:120547800-120549800	Flanking Active TSS	HUVEC	blood vessel
37	chr4:120547800-120550400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr4:120547800-120550400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:120547800-120550400	Active TSS	Brain Angular Gyrus	brain
40	chr4:120547800-120550400	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr4:120547800-120550400	Active TSS	Small Intestine	intestine
42	chr4:120547800-120550400	Active TSS	Stomach Mucosa	stomach
43	chr4:120547800-120550400	Active TSS	HSMMtube	muscle
44	chr4:120547800-120550600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:120547800-120550600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr4:120547800-120550600	Active TSS	A549	lung
47	chr4:120547800-120550800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr4:120548000-120549800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:120548000-120549800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr4:120548000-120550200	Active TSS	Muscle Satellite Cultured Cells	--

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