Variant report

Variant	rs28656140
Chromosome Location	chr14:56047588-56047589
allele	C/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	chr14:56047349-56047985	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr14:56047301-56047600	ProgFib	skin:	n/a	n/a
3	MXI1	chr14:56045617-56048670	SK-N-SH	brain:	n/a	n/a
4	HEY1	chr14:56047408-56047951	HepG2	liver:	n/a	chr14:56047628-56047643
5	POLR2A	chr14:56046372-56048148	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr14:56047560-56047710	GM12871	blood:	n/a	chr14:56047590-56047603
7	CCNT2	chr14:56046541-56047888	K562	blood:	n/a	n/a
8	EP300	chr14:56047532-56048420	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:56046464-56047942	NB4	blood:	n/a	n/a
10	MTA3	chr14:56047267-56048361	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:56046376-56048101	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr14:56047166-56047768	GM12878	blood:	n/a	n/a
13	CTCF	chr14:56047460-56047610	GM12864	blood:	n/a	chr14:56047590-56047603
14	CTCF	chr14:56047520-56047670	GM12875	blood:	n/a	chr14:56047590-56047603
15	YY1	chr14:56047184-56047748	GM12878	blood:	n/a	chr14:56047629-56047640
16	CTCF	chr14:56047500-56047650	AoAF	blood vessel:	n/a	chr14:56047590-56047603
17	CTCF	chr14:56047520-56047670	HEEpiC	esophagus:	n/a	chr14:56047590-56047603
18	GATA2	chr14:56047533-56048583	SH-SY5Y	brain:	n/a	chr14:56048312-56048326 chr14:56048043-56048053 chr14:56047750-56047760 chr14:56048313-56048322
19	POLR2A	chr14:56047384-56047961	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr14:56046367-56048084	GM18951	blood:	n/a	n/a
21	POLR2A	chr14:56046294-56048539	Hela-S3	cervix:	n/a	n/a
22	CHD2	chr14:56047362-56047863	HepG2	liver:	n/a	chr14:56047666-56047676
23	CTCF	chr14:56047480-56047630	GM12873	blood:	n/a	chr14:56047590-56047603
24	MAX	chr14:56046384-56048146	HepG2	liver:	n/a	chr14:56047371-56047381
25	CTCF	chr14:56047500-56047650	GM12865	blood:	n/a	chr14:56047590-56047603
26	CHD2	chr14:56047381-56047969	K562	blood:	n/a	chr14:56047666-56047676
27	MAZ	chr14:56046395-56047911	GM12878	blood:	n/a	chr14:56047371-56047381
28	ELF1	chr14:56046501-56047871	GM12878	blood:	n/a	chr14:56046829-56046841 chr14:56046868-56046880 chr14:56046875-56046884
29	HA-E2F1	chr14:56046651-56047679	Hela-S3	cervix:	n/a	chr14:56046870-56046880 chr14:56047276-56047285 chr14:56047027-56047037
30	CTCF	chr14:56047480-56047630	SAEC	small airway:	n/a	chr14:56047590-56047603
31	POLR2A	chr14:56046553-56048034	HepG2	liver:	n/a	n/a
32	MAX	chr14:56047378-56048114	GM12878	blood:	n/a	n/a
33	CTCF	chr14:56047520-56047670	GM12868	blood:	n/a	chr14:56047590-56047603
34	POLR2A	chr14:56046547-56047645	A549	lung:	n/a	n/a
35	CHD2	chr14:56047368-56048028	Hela-S3	cervix:	n/a	chr14:56047666-56047676
36	TCF12	chr14:56047322-56048266	A549	lung:	n/a	n/a
37	CTCF	chr14:56047520-56047670	GM12873	blood:	n/a	chr14:56047590-56047603
38	MXI1	chr14:56046386-56048303	GM12878	blood:	n/a	n/a
39	CTCF	chr14:56047580-56047730	GM12878	blood:	n/a	chr14:56047590-56047603
40	TCF12	chr14:56046348-56048005	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr14:56047186-56048256	A549	lung:	n/a	chr14:56047371-56047381
42	E2F6	chr14:56047399-56047623	K562	blood:	n/a	n/a
43	POLR2A	chr14:56047271-56047633	K562	blood:	n/a	n/a
44	SMARCB1	chr14:56045893-56048114	Hela-S3	cervix:	n/a	n/a
45	TCF7L2	chr14:56046452-56047940	HCT-116	colon:	n/a	n/a
46	POLR2A	chr14:56047376-56047608	A549	lung:	n/a	n/a
47	YY1	chr14:56047330-56047757	H1-hESC	embryonic stem cell:	n/a	chr14:56047629-56047640
48	POLR2A	chr14:56046415-56047808	K562	blood:	n/a	n/a
49	CTCF	chr14:56047440-56047590	GM12868	blood:	n/a	n/a
50	CTCF	chr14:56047500-56047650	Caco-2	colon:	n/a	chr14:56047590-56047603

No.	Distal block	Cell Line	Cell type
1	chr14:55737342..55739119-chr14:56046136..56048438,2	K562	blood:
2	chr1:151964961..151965492-chr14:56046820..56047820,2	Hela-S3	cervix:
3	chr14:56047540..56051954-chr14:56053859..56059782,6	K562	blood:
4	chr14:56022620..56026445-chr14:56044953..56047966,3	MCF-7	breast:
5	chr14:56046884..56048461-chr14:56110849..56113567,2	K562	blood:
6	chr14:56046559..56049206-chr14:56078372..56080917,2	MCF-7	breast:

Variant related genes	Relation type
KTN1-AS1	TF binding region
ENSG00000258413	Chromatin interaction
ENSG00000126777	Chromatin interaction
ENSG00000178974	Chromatin interaction
ENSG00000197747	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10083493	0.94[AFR][1000 genomes]
rs10135509	1.00[EUR][1000 genomes]
rs10140432	1.00[AMR][1000 genomes]
rs10142497	0.94[AFR][1000 genomes]
rs10142739	1.00[AMR][1000 genomes]
rs10142757	0.82[AFR][1000 genomes]
rs10143002	0.80[AFR][1000 genomes]
rs10146604	0.86[AFR][1000 genomes]
rs10148188	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10148983	0.82[AFR][1000 genomes]
rs10149408	0.86[AFR][1000 genomes]
rs13379264	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13379342	0.82[AFR][1000 genomes]
rs13379343	0.88[AFR][1000 genomes]
rs17683656	0.82[AFR][1000 genomes]
rs28366673	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28373835	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28409547	0.91[AFR][1000 genomes]
rs28478195	0.94[AFR][1000 genomes]
rs28534706	1.00[EUR][1000 genomes]
rs28558467	1.00[EUR][1000 genomes]
rs9944028	0.82[AFR][1000 genomes]
rs9972178	0.82[AFR][1000 genomes]
rs9972180	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv3375073	chr14:56045749-56048597	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3345234	chr14:56045824-56048372	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56045200-56048000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr14:56045200-56048200	Active TSS	NHDF-Ad	bronchial
3	chr14:56045200-56048400	Active TSS	Ovary	ovary
4	chr14:56045200-56048400	Active TSS	A549	lung
5	chr14:56045200-56050000	Active TSS	GM12878-XiMat	blood
6	chr14:56045400-56047800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:56045400-56047800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr14:56045400-56048000	Active TSS	Brain Cingulate Gyrus	brain
9	chr14:56045400-56048000	Active TSS	Brain Hippocampus Middle	brain
10	chr14:56045400-56048000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr14:56045400-56048000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr14:56045400-56048000	Active TSS	Right Ventricle	heart
13	chr14:56045400-56048200	Active TSS	HMEC	breast
14	chr14:56045400-56048400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:56045600-56047600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:56045600-56048000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr14:56045600-56048000	Active TSS	Brain Anterior Caudate	brain
18	chr14:56045600-56048000	Active TSS	Fetal Intestine Large	intestine
19	chr14:56045600-56048200	Active TSS	Colon Smooth Muscle	Colon
20	chr14:56045600-56048200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr14:56045600-56048200	Active TSS	Rectal Smooth Muscle	rectum
22	chr14:56045600-56048400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr14:56045600-56048400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:56045600-56048400	Active TSS	Pancreas	Pancrea
25	chr14:56045600-56048600	Active TSS	H9 Cell Line	embryonic stem cell
26	chr14:56045600-56048800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr14:56045600-56048800	Active TSS	NHLF	lung
28	chr14:56045600-56049000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:56045600-56050000	Active TSS	Right Atrium	heart
30	chr14:56045600-56051000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr14:56045800-56047800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:56045800-56047800	Active TSS	Liver	Liver
33	chr14:56045800-56047800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr14:56045800-56047800	Active TSS	Fetal Lung	lung
35	chr14:56045800-56047800	Active TSS	Spleen	Spleen
36	chr14:56045800-56048200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr14:56045800-56048200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr14:56045800-56048200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr14:56045800-56048200	Active TSS	Aorta	Aorta
40	chr14:56045800-56048200	Active TSS	Esophagus	oesophagus
41	chr14:56045800-56048400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr14:56045800-56048400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr14:56045800-56048400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr14:56045800-56048400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr14:56045800-56048400	Active TSS	Psoas Muscle	Psoas
46	chr14:56045800-56048600	Active TSS	Colonic Mucosa	Colon
47	chr14:56046000-56047600	Active TSS	Stomach Mucosa	stomach
48	chr14:56046000-56047800	Active TSS	Brain Angular Gyrus	brain
49	chr14:56046000-56047800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr14:56046000-56047800	Active TSS	HUVEC	blood vessel

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