Variant report

Variant	rs13220817
Chromosome Location	chr6:27356527-27356528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:386)
CpG islands
(count:183)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:386 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr6:27356096-27357080	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPD	chr6:27356331-27356922	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr6:27356269-27357118	K562	blood:	n/a	n/a
4	TCF12	chr6:27356489-27356905	A549	lung:	n/a	n/a
5	BCLAF1	chr6:27356365-27356967	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:27356252-27357091	Gliobla	brain:	n/a	n/a
7	YY1	chr6:27356518-27356950	GM12891	blood:	n/a	n/a
8	TAF1	chr6:27356402-27356882	HepG2	liver:	n/a	n/a
9	TAF1	chr6:27356205-27356945	K562	blood:	n/a	n/a
10	RUNX3	chr6:27356285-27357228	GM12878	blood:	n/a	n/a
11	ATF3	chr6:27356390-27356930	A549	lung:	n/a	n/a
12	CTCF	chr6:27356401-27356864	K562	blood:	n/a	n/a
13	RAD21	chr6:27356407-27356839	H1-hESC	embryonic stem cell:	n/a	chr6:27356420-27356430
14	POLR2A	chr6:27356313-27357014	GM12891	blood:	n/a	n/a
15	HCFC1	chr6:27355949-27357120	Hela-S3	cervix:	n/a	n/a
16	GABPA	chr6:27356527-27356932	H1-hESC	embryonic stem cell:	n/a	chr6:27356879-27356886
17	ATF3	chr6:27356439-27356968	K562	blood:	n/a	n/a
18	SIN3AK20	chr6:27356297-27357046	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr6:27356304-27356910	HepG2	liver:	n/a	n/a
20	ZBTB7A	chr6:27356140-27357034	K562	blood:	n/a	n/a
21	ATF2	chr6:27356395-27356962	H1-hESC	embryonic stem cell:	n/a	n/a
22	SIN3A	chr6:27356193-27357095	H1-hESC	embryonic stem cell:	n/a	n/a
23	SETDB1	chr6:27356287-27356944	U2OS	brain:	n/a	chr6:27356492-27356501
24	MAX	chr6:27355707-27357130	NB4	blood:	n/a	chr6:27356374-27356384 chr6:27356973-27356982
25	POLR2A	chr6:27356319-27356931	HUVEC	blood vessel:	n/a	n/a
26	RFX5	chr6:27356516-27356851	H1-hESC	embryonic stem cell:	n/a	n/a
27	USF1	chr6:27356452-27356853	K562	blood:	n/a	n/a
28	TAF7	chr6:27356520-27356823	K562	blood:	n/a	n/a
29	FOS	chr6:27356433-27356723	MCF10A-Er-Src	breast:	n/a	n/a
30	RFX5	chr6:27356489-27356890	Hela-S3	cervix:	n/a	n/a
31	ZNF263	chr6:27356264-27356940	HEK293-T-REx	kidney:	n/a	n/a
32	MYC	chr6:27356113-27357175	NB4	blood:	n/a	chr6:27356374-27356384 chr6:27356973-27356982
33	POLR2A	chr6:27356312-27356944	GM12892	blood:	n/a	n/a
34	IRF4	chr6:27356338-27356902	GM12878	blood:	n/a	n/a
35	NRF1	chr6:27356070-27357403	SK-N-SH	brain:	n/a	chr6:27356879-27356886 chr6:27356491-27356505 chr6:27356491-27356502 chr6:27356490-27356501
36	TAF1	chr6:27356078-27356992	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr6:27356305-27357066	GM12878	blood:	n/a	n/a
38	YY1	chr6:27356504-27356947	GM12892	blood:	n/a	n/a
39	POLR2A	chr6:27356296-27357027	K562	blood:	n/a	n/a
40	POLR2A	chr6:27356447-27356997	MCF10A-Er-Src	breast:	n/a	n/a
41	YY1	chr6:27356405-27356954	GM12878	blood:	n/a	n/a
42	MAZ	chr6:27356327-27356915	Hela-S3	cervix:	n/a	chr6:27356374-27356384
43	POLR2A	chr6:27356350-27356954	HepG2	liver:	n/a	n/a
44	SMC3	chr6:27356440-27356912	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:27356371-27356842	A549	lung:	n/a	n/a
46	NR2F2	chr6:27356243-27357073	K562	blood:	n/a	n/a
47	TAF1	chr6:27356477-27356897	GM12878	blood:	n/a	n/a
48	REST	chr6:27356271-27356975	A549	lung:	n/a	chr6:27356858-27356878
49	CEBPB	chr6:27355943-27356733	K562	blood:	n/a	chr6:27356124-27356135 chr6:27356433-27356444 chr6:27355981-27355990 chr6:27356126-27356135
50	GABPA	chr6:27356492-27356888	Hela-S3	cervix:	n/a	chr6:27356879-27356886

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27356499-27356549	HepG2	liver:	n/a
2	chr6:27356513-27356563	HCPEpiC	choroid plexus:	n/a
3	chr6:27356499-27356549	HEEpiC	esophagus:	n/a
4	chr6:27356499-27356549	HRPEpiC	eye:	n/a
5	chr6:27356513-27356563	MCF10A-Er-Src	breast:	n/a
6	chr6:27356509-27356559	MCF-7	breast:	n/a
7	chr6:27356509-27356559	HCF	heart:	n/a
8	chr6:27356499-27356549	GM12891	blood:	n/a
9	chr6:27356509-27356559	PANC-1	pancreas:	n/a
10	chr6:27356513-27356563	MCF-7	breast:	n/a
11	chr6:27356513-27356563	Hela-S3	cervix:	n/a
12	chr6:27356499-27356549	SK-N-MC	brain:	n/a
13	chr6:27356509-27356559	AoSMC	blood vessel:	n/a
14	chr6:27356509-27356559	IMR90	lung:	fetal
15	chr6:27356509-27356559	GM12891	blood:	n/a
16	chr6:27356513-27356563	T-47D	breast:	n/a
17	chr6:27356513-27356563	GM12892	blood:	n/a
18	chr6:27356513-27356563	Caco-2	colon:	n/a
19	chr6:27356513-27356563	BE2_C	brain:	n/a
20	chr6:27356499-27356549	HRE	kidney:	n/a
21	chr6:27356499-27356549	HRCEpiC	kidney:	n/a
22	chr6:27356513-27356563	HEEpiC	esophagus:	n/a
23	chr6:27356513-27356563	SK-N-MC	brain:	n/a
24	chr6:27356499-27356549	BE2_C	brain:	n/a
25	chr6:27356513-27356563	HepG2	liver:	n/a
26	chr6:27356509-27356559	HNPCEpiC	eye:	n/a
27	chr6:27356509-27356559	SKMC	muscle:	n/a
28	chr6:27356509-27356559	HEK293	kidney:	embryo
29	chr6:27356509-27356559	HCT-116	colon:	n/a
30	chr6:27356513-27356563	AG04449	skin:	fetal
31	chr6:27356513-27356563	HUVEC	blood vessel:	n/a
32	chr6:27356513-27356563	HNPCEpiC	eye:	n/a
33	chr6:27356509-27356559	Caco-2	colon:	n/a
34	chr6:27356509-27356559	AG04450	lung:	fetal
35	chr6:27356499-27356549	SAEC	small airway:	n/a
36	chr6:27356509-27356559	BJ	skin:	n/a
37	chr6:27356499-27356549	LNCaP	prostate:	n/a
38	chr6:27356509-27356559	T-47D	breast:	n/a
39	chr6:27356513-27356563	NHBE	bronchial:	n/a
40	chr6:27356513-27356563	HMEC	breast:	n/a
41	chr6:27356509-27356559	HUVEC	blood vessel:	n/a
42	chr6:27356499-27356549	Caco-2	colon:	n/a
43	chr6:27356513-27356563	RPTEC	kidney:	n/a
44	chr6:27356499-27356549	RPTEC	kidney:	n/a
45	chr6:27356513-27356563	LNCaP	prostate:	n/a
46	chr6:27356509-27356559	ProgFib	skin:	n/a
47	chr6:27356509-27356559	HRCEpiC	kidney:	n/a
48	chr6:27356513-27356563	CMK	blood:	n/a
49	chr6:27356513-27356563	BJ	skin:	n/a
50	chr6:27356509-27356559	HCPEpiC	choroid plexus:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27113785..27116304-chr6:27356399..27358052,2	K562	blood:
2	chr6:27356277..27359093-chr6:27439899..27443040,4	MCF-7	breast:
3	chr6:27354651..27357206-chr6:27439212..27442131,3	K562	blood:
4	chr6:27356362..27358956-chr6:27773296..27775539,3	K562	blood:
5	chr6:27341304..27343058-chr6:27356076..27357820,2	MCF-7	breast:
6	chr21:27542816..27543374-chr6:27355736..27356540,2	HCT-116	colon:
7	chr6:27342371..27343890-chr6:27355850..27358027,2	K562	blood:
8	chr6:27291445..27294642-chr6:27355178..27358043,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF184-3	chr6:27356046-27357004	NONHSAT108378

No data

Variant related genes	Relation type
ZNF391	TF binding region
ZNF391	CpG island
ENSG00000265565	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000220758	Chromatin interaction
ENSG00000273492	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000142192	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1011665	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10946915	0.95[ASN][1000 genomes]
rs12526495	0.88[ASN][1000 genomes]
rs12529458	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs12662076	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs12663650	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12664996	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1883403	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2064093	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs2206250	0.83[CHD][hapmap]
rs2235232	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2393926	0.97[ASN][1000 genomes]
rs2393962	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs2393964	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs4711152	0.92[ASN][1000 genomes]
rs4713098	0.84[ASN][1000 genomes]
rs4713099	0.84[ASN][1000 genomes]
rs6913166	1.00[ASW][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914864	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6922815	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71559025	0.84[ASN][1000 genomes]
rs764284	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754977	0.91[YRI][hapmap]
rs7761966	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs7772739	0.97[ASN][1000 genomes]
rs9357038	0.94[ASN][1000 genomes]
rs9379980	0.84[ASN][1000 genomes]
rs9393813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3439048	chr6:27351973-27357171	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
4	nsv1031803	chr6:27355881-27423655	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv538166	chr6:27355881-27423655	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv517557	chr6:27356527-27356925	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13220817	ZNF391	cis	cerebellum	SCAN
rs13220817	ZSCAN23	cis	cerebellum	SCAN
rs13220817	ZNF391	cis	Muscle Skeletal	GTEx
rs13220817	ZNF391	cis	lung	GTEx
rs13220817	HIST1H3B	cis	cerebellum	SCAN
rs13220817	ZNF391	cis	Artery Tibial	GTEx
rs13220817	ZNF204P	cis	cerebellum	SCAN
rs13220817	ZNF391	cis	lymphoblastoid	seeQTL
rs13220817	ZNF391	cis	Esophagus Muscularis	GTEx
rs13220817	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs13220817	ZNF204P	cis	parietal	SCAN
rs13220817	ZNF391	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27355000-27357400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:27355600-27357600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr6:27355600-27358400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:27355800-27356600	Active TSS	Fetal Muscle Trunk	muscle
5	chr6:27355800-27356800	Active TSS	Colonic Mucosa	Colon
6	chr6:27355800-27357000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:27355800-27357000	Active TSS	Brain Angular Gyrus	brain
8	chr6:27355800-27357000	Active TSS	HMEC	breast
9	chr6:27355800-27357200	Active TSS	Muscle Satellite Cultured Cells	--
10	chr6:27355800-27357200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:27355800-27357200	Active TSS	Aorta	Aorta
12	chr6:27355800-27357200	Active TSS	Brain Hippocampus Middle	brain
13	chr6:27355800-27357200	Active TSS	Fetal Brain Male	brain
14	chr6:27355800-27357200	Active TSS	Right Ventricle	heart
15	chr6:27355800-27357200	Active TSS	A549	lung
16	chr6:27355800-27357200	Flanking Active TSS	HUVEC	blood vessel
17	chr6:27355800-27357200	Active TSS	K562	blood
18	chr6:27355800-27357200	Active TSS	NHDF-Ad	bronchial
19	chr6:27355800-27357400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:27355800-27357400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:27355800-27357400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:27355800-27357400	Active TSS	Brain Cingulate Gyrus	brain
23	chr6:27355800-27357400	Active TSS	Fetal Brain Female	brain
24	chr6:27355800-27357400	Active TSS	Fetal Intestine Small	intestine
25	chr6:27355800-27357400	Active TSS	Rectal Smooth Muscle	rectum
26	chr6:27355800-27357400	Active TSS	NHLF	lung
27	chr6:27355800-27357600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr6:27355800-27357600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:27355800-27357600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:27355800-27357600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:27355800-27357600	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr6:27355800-27357600	Active TSS	Stomach Smooth Muscle	stomach
33	chr6:27355800-27357600	Active TSS	NHEK	skin
34	chr6:27355800-27357800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr6:27355800-27357800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr6:27355800-27357800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:27355800-27357800	Active TSS	GM12878-XiMat	blood
38	chr6:27355800-27358000	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:27355800-27358000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:27356000-27356600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr6:27356000-27356600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr6:27356000-27356800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:27356000-27356800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:27356000-27356800	Active TSS	Thymus	Thymus
45	chr6:27356000-27356800	Bivalent/Poised TSS	HepG2	liver
46	chr6:27356000-27357000	Active TSS	Fetal Lung	lung
47	chr6:27356000-27357000	Active TSS	Left Ventricle	heart
48	chr6:27356000-27357000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:27356000-27357000	Active TSS	HSMMtube	muscle
50	chr6:27356000-27357200	Active TSS	Primary T killer memory cells from peripheral blood	blood

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