Variant report

Variant	rs2252745
Chromosome Location	chr6:30579315-30579316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30578658-30579827	K562	blood:	n/a	n/a
2	POLR2A	chr6:30576348-30586731	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr6:30576459-30586534	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:30579296-30585245	U87	brain:	n/a	n/a
5	POLR2A	chr6:30576762-30586531	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:30576975-30579686	K562	blood:	n/a	n/a
7	POLR2A	chr6:30576843-30586279	HCT-116	colon:	n/a	n/a
8	POLR2A	chr6:30579276-30579727	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:30576894-30586563	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr6:30579091-30586493	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:30579199-30585823	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:30576267-30586793	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr6:30576421-30586088	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr6:30576151-30586136	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:30576533-30586585	GM12891	blood:	n/a	n/a
16	POLR2A	chr6:30579278-30579777	HCT-116	colon:	n/a	n/a
17	POLR2A	chr6:30576971-30585965	U87	brain:	n/a	n/a
18	POLR2A	chr6:30579016-30586553	K562	blood:	n/a	n/a
19	POLR2A	chr6:30576897-30586493	K562	blood:	n/a	n/a
20	POLR2A	chr6:30576601-30586578	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:30577488-30586361	PBDE	blood:	n/a	n/a
22	POLR2A	chr6:30579299-30586198	K562	blood:	n/a	n/a
23	POLR2A	chr6:30576348-30586293	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr6:30579237-30586140	GM18505	blood:	n/a	n/a
25	POLR2A	chr6:30577342-30579349	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:30579310-30579699	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr6:30578692-30586507	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr6:30579282-30579493	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr6:30576539-30586508	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr6:30576353-30586641	PFSK-1	brain:	n/a	n/a
31	NFATC1	chr6:30579009-30580177	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:30576529-30586246	MCF-7	breast:	n/a	n/a
33	POLR2A	chr6:30576404-30586729	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr6:30575677-30585966	HepG2	liver:	n/a	n/a
35	POLR2A	chr6:30576695-30579733	K562	blood:	n/a	n/a
36	POLR2A	chr6:30577524-30586495	K562	blood:	n/a	n/a
37	POLR2A	chr6:30576673-30586586	HepG2	liver:	n/a	n/a
38	POLR2A	chr6:30576922-30586466	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr6:30576678-30585977	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr6:30576540-30585908	K562	blood:	n/a	n/a
41	POLR2A	chr6:30576965-30586055	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30579288-30579338	NHBE	bronchial:	n/a
2	chr6:30579288-30579338	HNPCEpiC	eye:	n/a
3	chr6:30579288-30579338	NT2-D1	testis:	n/a
4	chr6:30579288-30579338	MCF10A-Er-Src	breast:	n/a
5	chr6:30579288-30579338	AoSMC	blood vessel:	n/a
6	chr6:30579288-30579338	AG09309	skin:	n/a
7	chr6:30579288-30579338	NB4	blood:	n/a
8	chr6:30579288-30579338	ovcar-3	ovarian:	n/a
9	chr6:30579288-30579338	MCF-7	breast:	n/a
10	chr6:30579288-30579338	LNCaP	prostate:	n/a
11	chr6:30579288-30579338	GM12878	blood:	n/a
12	chr6:30579288-30579338	HRCEpiC	kidney:	n/a
13	chr6:30579288-30579338	Hepatocyte	liver:	n/a
14	chr6:30579288-30579338	HCM	heart:	n/a
15	chr6:30579288-30579338	SK-N-SH_RA	brain:	n/a
16	chr6:30579288-30579338	AG10803	skin:	n/a
17	chr6:30579288-30579338	NHDF-neo	bronchial:	n/a
18	chr6:30579288-30579338	BJ	skin:	n/a
19	chr6:30579288-30579338	GM12892	blood:	n/a
20	chr6:30579288-30579338	HMEC	breast:	n/a
21	chr6:30579288-30579338	HRE	kidney:	n/a
22	chr6:30579288-30579338	SKMC	muscle:	n/a
23	chr6:30579288-30579338	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:30579288-30579338	GM06990	blood:	n/a
25	chr6:30579288-30579338	HCF	heart:	n/a
26	chr6:30579288-30579338	HCT-116	colon:	n/a
27	chr6:30579288-30579338	HUVEC	blood vessel:	n/a
28	chr6:30579288-30579338	Jurkat	blood:	n/a
29	chr6:30579288-30579338	PFSK-1	brain:	n/a
30	chr6:30579288-30579338	Caco-2	colon:	n/a
31	chr6:30579288-30579338	AG04450	lung:	fetal
32	chr6:30579288-30579338	U87	brain:	n/a
33	chr6:30579288-30579338	RPTEC	kidney:	n/a
34	chr6:30579288-30579338	HAEpiC	amniotic membrane:	n/a
35	chr6:30579288-30579338	HIPEpiC	eye:	n/a
36	chr6:30579288-30579338	Hela-S3	cervix:	n/a
37	chr6:30579288-30579338	AG09319	gingival:	n/a
38	chr6:30579288-30579338	PANC-1	pancreas:	n/a
39	chr6:30579288-30579338	AG04449	skin:	fetal
40	chr6:30579288-30579338	ProgFib	skin:	n/a
41	chr6:30579288-30579338	HEK293	kidney:	embryo
42	chr6:30579288-30579338	IMR90	lung:	fetal
43	chr6:30579288-30579338	HL-60	blood:	n/a
44	chr6:30579288-30579338	GM19239	blood:	n/a
45	chr6:30579288-30579338	H1-hESC	embryonic stem cell:	embryo
46	chr6:30579288-30579338	HRPEpiC	eye:	n/a
47	chr6:30579288-30579338	GM12891	blood:	n/a
48	chr6:30579288-30579338	SK-N-SH	brain:	n/a
49	chr6:30579288-30579338	SAEC	small airway:	n/a
50	chr6:30579288-30579338	HEEpiC	esophagus:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:
2	chr6:30579085..30581613-chr6:30852854..30854555,2	MCF-7	breast:
3	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
4	chr6:30577127..30589352-chr6:30620628..30648657,88	K562	blood:
5	chr6:30452366..30463564-chr6:30577885..30586736,19	MCF-7	breast:
6	chr6:30537301..30541414-chr6:30578056..30586798,20	MCF-7	breast:
7	chr2:79645281..79647145-chr6:30579289..30582193,2	MCF-7	breast:
8	chr6:30511109..30514018-chr6:30576685..30580337,3	MCF-7	breast:
9	chr6:30520810..30527475-chr6:30577152..30588201,32	MCF-7	breast:
10	chr6:30577364..30581812-chr6:30612731..30615596,7	MCF-7	breast:
11	chr17:56735195..56737816-chr6:30578332..30581180,2	MCF-7	breast:
12	chr6:30576975..30585099-chr6:30622978..30628754,9	MCF-7	breast:
13	chr3:105586480..105589335-chr6:30578433..30580821,2	K562	blood:
14	chr6:30501371..30504136-chr6:30577423..30580435,3	K562	blood:
15	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
16	chr6:30517868..30527565-chr6:30576812..30587078,24	MCF-7	breast:
17	chr6:30578948..30585851-chr6:30707403..30713755,14	MCF-7	breast:
18	chr6:30511425..30515490-chr6:30579291..30582937,6	MCF-7	breast:

No data

Variant related genes	Relation type
PPP1R10	TF binding region
PPP1R10	CpG island
ENSG00000204592	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000114423	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000236603	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1058318	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1140809	0.90[AFR][1000 genomes]
rs12174151	0.90[ASN][1000 genomes]
rs1264419	0.94[AFR][1000 genomes]
rs1264421	0.90[AFR][1000 genomes]
rs1264423	0.94[AFR][1000 genomes]
rs1264432	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264437	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1264438	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264439	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1264440	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1264448	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1264456	0.81[EUR][1000 genomes]
rs12665339	0.82[ASN][1000 genomes]
rs1362119	0.82[EUR][1000 genomes]
rs2074503	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2074504	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2074505	0.81[EUR][1000 genomes]
rs2269709	0.82[EUR][1000 genomes]
rs2516639	0.83[EUR][1000 genomes]
rs2516641	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2516642	0.81[EUR][1000 genomes]
rs2516643	0.82[EUR][1000 genomes]
rs2516644	0.82[EUR][1000 genomes]
rs2516646	0.81[EUR][1000 genomes]
rs2516649	0.81[EUR][1000 genomes]
rs2524223	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2524226	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534803	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2534804	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2534805	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2534808	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2534814	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2534815	0.82[EUR][1000 genomes]
rs2534817	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2534820	0.81[EUR][1000 genomes]
rs2534821	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2534823	0.80[EUR][1000 genomes]
rs2844723	0.80[EUR][1000 genomes]
rs3094718	0.82[EUR][1000 genomes]
rs3130039	0.81[EUR][1000 genomes]
rs3130041	0.81[EUR][1000 genomes]
rs3130045	0.81[EUR][1000 genomes]
rs3130240	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130242	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130243	0.81[EUR][1000 genomes]
rs3132612	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3132613	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132614	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9262118	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases
8	nsv5244	chr6:30545111-30589803	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	772 gene(s)	inside rSNPs	diseases
9	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2252745	HLA-E	cis	multi-tissue	Pritchard
rs2252745	CCHCR1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30540200-30582200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30540200-30582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:30542200-30581800	Weak transcription	Right Atrium	heart
4	chr6:30566400-30581000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:30566600-30579600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:30567000-30579400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:30567000-30579600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr6:30567200-30579600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:30567400-30579800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:30567400-30580000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:30567400-30580200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:30567400-30580400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:30567600-30580400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:30568000-30580000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:30568000-30580200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:30568200-30579600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr6:30568200-30579800	Strong transcription	A549	lung
18	chr6:30568200-30579800	Strong transcription	NHEK	skin
19	chr6:30568400-30579600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:30568400-30580000	Strong transcription	K562	blood
21	chr6:30568400-30580800	Strong transcription	GM12878-XiMat	blood
22	chr6:30574600-30582200	Weak transcription	Small Intestine	intestine
23	chr6:30574600-30582400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:30575600-30579400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:30576200-30579400	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr6:30576400-30581600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:30576800-30579600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:30577000-30579400	Strong transcription	Placenta	Placenta
29	chr6:30577000-30580800	Genic enhancers	Primary B cells from cord blood	blood
30	chr6:30577000-30581800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr6:30577200-30579400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:30577200-30580600	Enhancers	Adipose Nuclei	Adipose
33	chr6:30577200-30580800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:30577200-30582000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr6:30577200-30582200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:30577400-30579600	Weak transcription	Stomach Mucosa	stomach
37	chr6:30577400-30580200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:30577400-30580400	Weak transcription	Fetal Brain Male	brain
39	chr6:30577400-30580400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:30577400-30580800	Weak transcription	Spleen	Spleen
41	chr6:30577400-30581000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:30577400-30582200	Weak transcription	Esophagus	oesophagus
43	chr6:30577400-30582200	Weak transcription	Lung	lung
44	chr6:30577400-30582200	Weak transcription	HSMMtube	muscle
45	chr6:30577600-30579400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:30577600-30579400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:30577600-30579400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:30577600-30579600	Genic enhancers	Osteobl	bone
49	chr6:30577600-30580000	Weak transcription	Colonic Mucosa	Colon
50	chr6:30577600-30580400	Weak transcription	Primary hematopoietic stem cells	blood

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