Variant report

Variant	rs2252040
Chromosome Location	chr14:39645863-39645864
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:39642960-39651251	H1-hESC	embryonic stem cell:	n/a	n/a
2	HEY1	chr14:39645676-39647521	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:39643051-39648902	HepG2	liver:	n/a	n/a
4	CHD1	chr14:39643798-39646129	H1-hESC	embryonic stem cell:	n/a	chr14:39644663-39644673
5	POLR2A	chr14:39645641-39647605	HepG2	liver:	n/a	n/a
6	POLR2A	chr14:39645593-39647104	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr14:39643261-39648811	K562	blood:	n/a	n/a
8	SREBP1	chr14:39643578-39645901	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:39645826-39647158	HepG2	liver:	n/a	n/a
10	MBD4	chr14:39643120-39646667	HepG2	liver:	n/a	n/a
11	TEAD4	chr14:39643084-39646101	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:39645594-39647030	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:39643730..39648156-chr14:39734640..39738499,10	MCF-7	breast:
2	chr14:39642546..39647225-chr14:39733415..39737853,13	MCF-7	breast:
3	chr14:39643409..39646477-chr14:39682252..39685201,4	MCF-7	breast:
4	chr14:39644686..39646338-chr14:39899658..39902040,2	K562	blood:

No data

Variant related genes	Relation type
PNN	TF binding region
ENSG00000259083	TF binding region
ENSG00000258940	Chromatin interaction
ENSG00000270503	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000165355	Chromatin interaction
ENSG00000258941	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10132034	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10132953	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10149829	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11157046	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11157047	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11157048	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434607	0.95[AMR][1000 genomes]
rs12895329	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs175341	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950509	0.88[AMR][1000 genomes]
rs1956629	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964842	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2038357	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2082637	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099410	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2180214	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2180217	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2180792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3899404	0.87[AFR][1000 genomes]
rs4290398	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616209	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902402	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902419	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902436	0.81[AMR][1000 genomes]
rs56163817	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6571889	0.88[AMR][1000 genomes]
rs6571890	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6571891	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6571894	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6571895	0.86[AMR][1000 genomes]
rs6571896	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571897	0.85[ASN][1000 genomes]
rs6571904	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6571905	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7147760	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154585	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs761804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003194	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8003485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8007063	0.89[AMR][1000 genomes]
rs8010111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8011855	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8012178	0.84[AFR][1000 genomes]
rs8014255	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021225	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022141	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9322993	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9671927	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 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	chr14:39643600-39646000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr14:39643600-39646000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr14:39643800-39646000	Active TSS	Sigmoid Colon	Sigmoid Colon
4	chr14:39643800-39646200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:39643800-39646600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:39644400-39646200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
7	chr14:39644400-39646200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
8	chr14:39644800-39646400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:39644800-39646600	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr14:39645000-39646400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
11	chr14:39645000-39646400	Transcr. at gene 5' and 3'	A549	lung
12	chr14:39645200-39646000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr14:39645200-39646200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:39645200-39646200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr14:39645200-39646200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
16	chr14:39645200-39646200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr14:39645200-39646200	Weak transcription	Spleen	Spleen
18	chr14:39645200-39646200	Transcr. at gene 5' and 3'	HMEC	breast
19	chr14:39645200-39646400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr14:39645200-39646400	Transcr. at gene 5' and 3'	NH-A	brain
21	chr14:39645200-39646600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
22	chr14:39645200-39646800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
23	chr14:39645200-39647000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
24	chr14:39645200-39647200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr14:39645400-39646000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr14:39645400-39646000	Enhancers	Primary B cells from peripheral blood	blood
27	chr14:39645400-39646000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
28	chr14:39645400-39646000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:39645400-39646200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:39645400-39646200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr14:39645400-39646200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:39645400-39646200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:39645400-39646200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:39645400-39646200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr14:39645400-39646200	Weak transcription	Aorta	Aorta
36	chr14:39645400-39646200	Enhancers	Brain Substantia Nigra	brain
37	chr14:39645400-39646200	Weak transcription	Colonic Mucosa	Colon
38	chr14:39645400-39646200	Weak transcription	Esophagus	oesophagus
39	chr14:39645400-39646200	Weak transcription	Left Ventricle	heart
40	chr14:39645400-39646200	Weak transcription	Ovary	ovary
41	chr14:39645400-39646200	Weak transcription	Pancreas	Pancrea
42	chr14:39645400-39646400	Weak transcription	Gastric	stomach
43	chr14:39645400-39646400	Weak transcription	Small Intestine	intestine
44	chr14:39645400-39646400	Enhancers	Stomach Mucosa	stomach
45	chr14:39645400-39646600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr14:39645400-39647000	Transcr. at gene 5' and 3'	Hela-S3	cervix
47	chr14:39645400-39647600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
48	chr14:39645400-39648000	Weak transcription	Fetal Brain Male	brain
49	chr14:39645400-39649000	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr14:39645600-39646000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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