Variant report

Variant	rs11970439
Chromosome Location	chr6:28303464-28303465
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:427)
CpG islands
(count:0)
Chromatin interactive
region (count:40)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:427 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZEB1	chr6:28303431-28304243	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:28302892-28305333	K562	blood:	n/a	n/a
3	CHD2	chr6:28302840-28304607	K562	blood:	n/a	n/a
4	SRF	chr6:28303100-28303546	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr6:28303280-28304197	GM18526	blood:	n/a	n/a
6	TBP	chr6:28303109-28304076	H1-hESC	embryonic stem cell:	n/a	n/a
7	RELA	chr6:28303163-28304527	GM19099	blood:	n/a	n/a
8	YY1	chr6:28303350-28304131	GM12878	blood:	n/a	n/a
9	FOSL2	chr6:28303103-28303579	MCF-7	breast:	n/a	chr6:28303396-28303407
10	CCNT2	chr6:28302797-28304559	K562	blood:	n/a	chr6:28304330-28304339 chr6:28303751-28303760
11	TAF1	chr6:28302853-28304712	H1-neurons	neurons:	n/a	n/a
12	EP300	chr6:28302761-28305309	K562	blood:	n/a	n/a
13	STAT5A	chr6:28302827-28304817	GM12878	blood:	n/a	chr6:28303817-28303825 chr6:28303984-28303998
14	MAZ	chr6:28303049-28304004	HepG2	liver:	n/a	n/a
15	BCLAF1	chr6:28303392-28304883	K562	blood:	n/a	chr6:28303752-28303761
16	FOSL2	chr6:28303202-28303555	A549	lung:	n/a	chr6:28303396-28303407
17	EGR1	chr6:28303399-28304082	K562	blood:	n/a	chr6:28303887-28303897 chr6:28303709-28303723 chr6:28303747-28303761
18	JUN	chr6:28302898-28304009	K562	blood:	n/a	n/a
19	RFX5	chr6:28303169-28303857	GM12878	blood:	n/a	n/a
20	MYBL2	chr6:28302986-28304302	HepG2	liver:	n/a	n/a
21	ELF1	chr6:28303424-28304073	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:28302941-28304723	GM12892	blood:	n/a	n/a
23	REST	chr6:28303358-28304663	HL-60	blood:	n/a	n/a
24	POLR2A	chr6:28303016-28304124	HepG2	liver:	n/a	n/a
25	SP1	chr6:28303107-28303621	GM12878	blood:	n/a	n/a
26	SP1	chr6:28303089-28304094	GM12878	blood:	n/a	chr6:28303750-28303762 chr6:28303752-28303761 chr6:28303750-28303762 chr6:28303747-28303761 chr6:28303699-28303711 chr6:28303751-28303760 chr6:28303701-28303710 chr6:28303699-28303711
27	MAFK	chr6:28303302-28303965	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr6:28303370-28304420	HepG2	liver:	n/a	n/a
29	MAX	chr6:28303361-28303990	H1-hESC	embryonic stem cell:	n/a	n/a
30	MXI1	chr6:28303169-28304240	H1-hESC	embryonic stem cell:	n/a	n/a
31	FOSL2	chr6:28303066-28303704	HepG2	liver:	n/a	chr6:28303396-28303407
32	YY1	chr6:28303289-28304054	HepG2	liver:	n/a	n/a
33	MAX	chr6:28303123-28304137	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr6:28303034-28304279	MCF-7	breast:	n/a	chr6:28303395-28303406 chr6:28304017-28304027
35	MAX	chr6:28303300-28304173	K562	blood:	n/a	n/a
36	CHD2	chr6:28303045-28304674	GM12878	blood:	n/a	n/a
37	MTA3	chr6:28302958-28304943	GM12878	blood:	n/a	n/a
38	SRF	chr6:28302866-28304064	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:28302808-28304634	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:28302740-28305408	K562	blood:	n/a	n/a
41	CEBPD	chr6:28303296-28304082	HepG2	liver:	n/a	n/a
42	POLR2A	chr6:28302926-28305211	GM12891	blood:	n/a	n/a
43	FOS	chr6:28302977-28304194	K562	blood:	n/a	chr6:28303395-28303406 chr6:28304017-28304027
44	ELK1	chr6:28303101-28304587	K562	blood:	n/a	n/a
45	HEY1	chr6:28303030-28304081	HepG2	liver:	n/a	n/a
46	JUN	chr6:28302649-28304752	K562	blood:	n/a	chr6:28304017-28304027
47	MXI1	chr6:28302942-28304803	K562	blood:	n/a	n/a
48	MAFF	chr6:28302915-28303651	K562	blood:	n/a	n/a
49	ATF1	chr6:28302803-28304590	K562	blood:	n/a	n/a
50	POLR2A	chr6:28303056-28304297	HUVEC	blood vessel:	n/a	n/a

No data

(count:40 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28109265..28112090-chr6:28302311..28305142,2	MCF-7	breast:
2	chr6:27775597..27780846-chr6:28300467..28304976,7	K562	blood:
3	chr6:28191649..28195458-chr6:28301378..28307708,9	K562	blood:
4	chr6:28303323..28305430-chr6:28323198..28325730,3	MCF-7	breast:
5	chr6:28099723..28110178-chr6:28301599..28306918,14	K562	blood:
6	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
7	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
8	chr6:27832606..27835088-chr6:28302807..28304572,2	K562	blood:
9	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
10	chr6:27832219..27835088-chr6:28302807..28305055,2	K562	blood:
11	chr6:28303262..28304846-chr9:91923985..91926684,2	MCF-7	breast:
12	chr6:27774293..27778194-chr6:28301096..28304976,3	K562	blood:
13	chr6:28109273..28111011-chr6:28302779..28305242,3	MCF-7	breast:
14	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
15	chr6:27798625..27800434-chr6:28302917..28305015,2	K562	blood:
16	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
17	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
18	chr6:28232839..28237434-chr6:28303380..28305726,5	MCF-7	breast:
19	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
20	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
21	chr12:125398287..125399124-chr6:28303371..28304159,3	Hela-S3	cervix:
22	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
23	chr6:27804731..27806517-chr6:28302178..28303810,2	MCF-7	breast:
24	chr12:125397947..125399800-chr6:28303115..28304778,2	K562	blood:
25	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
26	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
27	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
28	chr6:28302165..28304933-chr6:28366158..28368845,2	K562	blood:
29	chr6:28126892..28131515-chr6:28301205..28304944,6	K562	blood:
30	chr6:28232678..28234825-chr6:28301975..28304232,2	MCF-7	breast:
31	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:
32	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
33	chr6:28248171..28250694-chr6:28301952..28304469,4	MCF-7	breast:
34	chr6:28287491..28290035-chr6:28302948..28305431,2	K562	blood:
35	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
36	chr15:78832710..78833320-chr6:28303407..28304006,2	NB4	blood:
37	chr6:27802790..27806364-chr6:28301138..28304856,3	K562	blood:
38	chr6:27113242..27115485-chr6:28302941..28304550,2	K562	blood:
39	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
40	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000269293	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000198374	Chromatin interaction
ENSG00000041357	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000123975	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000270326	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000150991	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000226314	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1119211	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11756111	1.00[JPT][hapmap]
rs11758148	1.00[JPT][hapmap]
rs11758337	1.00[JPT][hapmap]
rs13210258	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1474589	1.00[JPT][hapmap]
rs16893937	1.00[JPT][hapmap]
rs17301128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17312661	0.94[CEU][hapmap]
rs17776284	1.00[JPT][hapmap]
rs2185955	1.00[JPT][hapmap]
rs2235358	1.00[JPT][hapmap]
rs2235359	1.00[JPT][hapmap]
rs2299031	1.00[JPT][hapmap]
rs2799081	0.80[EUR][1000 genomes]
rs35875412	0.80[EUR][1000 genomes]
rs3800326	1.00[JPT][hapmap]
rs56131013	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456814	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6456816	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6903652	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6903823	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6912584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6921919	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6922111	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs7766356	0.83[CEU][hapmap]
rs7769054	1.00[JPT][hapmap]
rs9468350	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs993619	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11970439	AL022393.7	cis	Muscle Skeletal	GTEx
rs11970439	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs11970439	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs11970439	ZSCAN23	cis	Artery Tibial	GTEx
rs11970439	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs11970439	ZSCAN23	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28302200-28305400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:28302400-28304400	Active TSS	HSMMtube	muscle
3	chr6:28302400-28305200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:28302400-28305200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:28302400-28305600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:28302600-28304200	Active TSS	Stomach Smooth Muscle	stomach
7	chr6:28302600-28304600	Active TSS	Colon Smooth Muscle	Colon
8	chr6:28302600-28305200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:28302600-28305200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:28302800-28303600	Active TSS	Primary B cells from cord blood	blood
11	chr6:28302800-28303600	Flanking Active TSS	Dnd41	blood
12	chr6:28302800-28303600	Active TSS	HMEC	breast
13	chr6:28302800-28304000	Active TSS	Muscle Satellite Cultured Cells	--
14	chr6:28302800-28304000	Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:28302800-28304000	Active TSS	Osteobl	bone
16	chr6:28302800-28304200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:28302800-28304200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:28302800-28304200	Active TSS	Primary T cells from cord blood	blood
19	chr6:28302800-28304200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:28302800-28304200	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:28302800-28304400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:28302800-28304400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:28302800-28304400	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:28302800-28304400	Active TSS	A549	lung
25	chr6:28302800-28304400	Active TSS	HSMM	muscle
26	chr6:28302800-28304800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr6:28302800-28304800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:28302800-28304800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:28302800-28304800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:28302800-28304800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:28302800-28304800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:28302800-28304800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:28302800-28304800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:28302800-28304800	Active TSS	Aorta	Aorta
35	chr6:28302800-28305000	Active TSS	Colonic Mucosa	Colon
36	chr6:28302800-28305000	Active TSS	Right Atrium	heart
37	chr6:28302800-28305000	Active TSS	Right Ventricle	heart
38	chr6:28302800-28305200	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr6:28302800-28305200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:28303000-28303600	Active TSS	HUVEC	blood vessel
41	chr6:28303000-28303800	Active TSS	Brain Germinal Matrix	brain
42	chr6:28303000-28304000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr6:28303000-28304000	Active TSS	Brain Angular Gyrus	brain
44	chr6:28303000-28304000	Active TSS	Hela-S3	cervix
45	chr6:28303000-28304200	Active TSS	Psoas Muscle	Psoas
46	chr6:28303000-28304200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:28303000-28304400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:28303000-28304400	Active TSS	Brain Hippocampus Middle	brain
49	chr6:28303000-28304400	Active TSS	Esophagus	oesophagus
50	chr6:28303000-28304400	Active TSS	Pancreas	Pancrea

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