Variant report

Variant	rs2120020
Chromosome Location	chr15:75316845-75316846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75315631-75316868	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr15:75315719-75316900	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:75315673-75316939	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:75315619-75316860	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr15:75315683-75317005	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:75315557-75316854	K562	blood:	n/a	n/a
7	POLR2A	chr15:75315730-75316896	GM12892	blood:	n/a	n/a
8	BCLAF1	chr15:75316372-75316860	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75315666-75316845	HL-60	blood:	n/a	n/a
10	STAT5A	chr15:75315591-75316847	GM12878	blood:	n/a	chr15:75316377-75316388
11	POLR2A	chr15:75316427-75316861	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:75315611-75316912	GM12892	blood:	n/a	n/a
13	MTA3	chr15:75315316-75316858	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:75315596-75316931	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr15:75314902-75317178	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:75315722-75316856	GM12891	blood:	n/a	n/a
17	POLR2A	chr15:75315568-75316856	HUVEC	blood vessel:	n/a	n/a
18	MAX	chr15:75315307-75316886	A549	lung:	n/a	chr15:75315975-75315985 chr15:75316627-75316642
19	POLR2A	chr15:75315662-75316994	GM12878	blood:	n/a	n/a
20	HCFC1	chr15:75315117-75316930	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:75315481-75317912	SK-N-MC	brain:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75315116..75318130-chr15:75502238..75505511,3	K562	blood:
2	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
3	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
4	chr15:75315988..75318426-chr15:75334585..75336329,2	K562	blood:
5	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
6	chr15:75316003..75319633-chr15:75325409..75329451,5	MCF-7	breast:
7	chr15:75316059..75318846-chr15:75482061..75483763,2	K562	blood:
8	chr15:75300826..75305111-chr15:75313603..75318752,6	MCF-7	breast:
9	chr15:75163895..75166026-chr15:75315159..75317542,2	MCF-7	breast:
10	chr15:75247469..75252493-chr15:75314645..75318771,7	MCF-7	breast:
11	chr15:75287417..75289225-chr15:75314885..75317439,2	MCF-7	breast:
12	chr15:75316439..75318954-chr15:75442453..75445329,2	K562	blood:
13	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
14	chr15:75302980..75304655-chr15:75315027..75317604,2	MCF-7	breast:
15	chr15:75246752..75249656-chr15:75313121..75316891,3	K562	blood:
16	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:

No data

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000178718	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000261779	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12185077	0.88[EUR][1000 genomes]
rs12185078	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12185102	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12324912	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12591119	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708514	0.81[AFR][1000 genomes]
rs12898259	0.88[AFR][1000 genomes]
rs12901243	0.88[AFR][1000 genomes]
rs12903201	0.88[AFR][1000 genomes]
rs12910644	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12911421	0.85[EUR][1000 genomes]
rs12917120	0.83[AFR][1000 genomes]
rs13056	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1867146	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083731	0.88[AFR][1000 genomes]
rs2120019	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289582	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2304903	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2415253	0.88[AFR][1000 genomes]
rs2415254	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2415255	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34237279	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34655806	0.88[AFR][1000 genomes]
rs34713999	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34835684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34913788	0.86[AFR][1000 genomes]
rs35577967	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35736167	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35911108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850093	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5020842	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59094290	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60425110	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6495147	0.87[AFR][1000 genomes]
rs67324798	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67544533	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7162900	0.87[AFR][1000 genomes]
rs7167285	0.86[AFR][1000 genomes]
rs7168680	0.87[AFR][1000 genomes]
rs7173833	0.88[AFR][1000 genomes]
rs7175720	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8028632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030089	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033837	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8033925	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036197	0.88[AFR][1000 genomes]
rs8036573	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8040169	0.88[AFR][1000 genomes]
rs8042409	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042558	0.81[ASN][1000 genomes]
rs9672995	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75315800-75317000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr15:75315800-75317000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:75315800-75317000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:75315800-75317200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75315800-75317600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:75315800-75317800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:75316200-75317600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:75316200-75318000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr15:75316400-75317000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:75316400-75317000	Flanking Active TSS	Rectal Smooth Muscle	rectum
11	chr15:75316400-75317000	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr15:75316400-75317000	Flanking Active TSS	Dnd41	blood
13	chr15:75316400-75317000	Flanking Active TSS	Hela-S3	cervix
14	chr15:75316400-75317200	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr15:75316400-75317200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr15:75316400-75317400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr15:75316400-75317800	Enhancers	Spleen	Spleen
18	chr15:75316600-75317000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:75316600-75317200	Enhancers	Primary B cells from cord blood	blood
20	chr15:75316600-75317200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr15:75316600-75317600	Enhancers	Primary B cells from peripheral blood	blood
22	chr15:75316600-75317800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr15:75316600-75317800	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr15:75316600-75317800	Enhancers	Pancreas	Pancrea
25	chr15:75316600-75318000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:75316600-75318000	Enhancers	Fetal Intestine Large	intestine
27	chr15:75316600-75318000	Enhancers	Lung	lung
28	chr15:75316600-75318200	Enhancers	Stomach Mucosa	stomach
29	chr15:75316600-75318400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:75316600-75321000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:75316600-75321000	Weak transcription	Brain Substantia Nigra	brain
32	chr15:75316600-75321600	Enhancers	Primary hematopoietic stem cells	blood
33	chr15:75316600-75321800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:75316600-75336800	Weak transcription	Fetal Brain Female	brain
35	chr15:75316800-75317000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr15:75316800-75317000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:75316800-75317000	Active TSS	Muscle Satellite Cultured Cells	--
38	chr15:75316800-75317000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:75316800-75317000	Active TSS	GM12878-XiMat	blood
40	chr15:75316800-75317200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:75316800-75317200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:75316800-75317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:75316800-75317200	Genic enhancers	Fetal Stomach	stomach
44	chr15:75316800-75317200	Enhancers	Thymus	Thymus
45	chr15:75316800-75317200	Active TSS	NHEK	skin
46	chr15:75316800-75317400	Enhancers	Colon Smooth Muscle	Colon
47	chr15:75316800-75317400	Weak transcription	Fetal Heart	heart
48	chr15:75316800-75317400	Enhancers	Fetal Intestine Small	intestine
49	chr15:75316800-75317400	Enhancers	Fetal Muscle Trunk	muscle
50	chr15:75316800-75317400	Enhancers	Placenta	Placenta

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