Variant report

Variant	rs723475
Chromosome Location	chr6:28304841-28304842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28302892-28305333	K562	blood:	n/a	n/a
2	CEBPB	chr6:28304053-28304853	K562	blood:	n/a	n/a
3	EP300	chr6:28302761-28305309	K562	blood:	n/a	n/a
4	BCLAF1	chr6:28303392-28304883	K562	blood:	n/a	chr6:28303752-28303761
5	MTA3	chr6:28302958-28304943	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:28302740-28305408	K562	blood:	n/a	n/a
7	POLR2A	chr6:28302926-28305211	GM12891	blood:	n/a	n/a
8	RFX5	chr6:28302436-28305318	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr6:28302881-28305223	K562	blood:	n/a	n/a
10	PML	chr6:28302267-28305304	K562	blood:	n/a	n/a
11	CUX1	chr6:28302926-28304842	K562	blood:	n/a	n/a
12	RELA	chr6:28303111-28304863	GM18505	blood:	n/a	n/a
13	NFIC	chr6:28303075-28304848	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:28303046-28305232	GM12878	blood:	n/a	n/a
15	TEAD4	chr6:28302119-28305609	K562	blood:	n/a	n/a
16	POLR2A	chr6:28302952-28304995	PANC-1	pancreas:	n/a	n/a
17	TBL1XR1	chr6:28302835-28305371	K562	blood:	n/a	n/a
18	RUNX3	chr6:28303019-28304959	GM12878	blood:	n/a	chr6:28304661-28304670 chr6:28303919-28303936 chr6:28304661-28304670 chr6:28303919-28303928 chr6:28303919-28303928
19	JUN	chr6:28300330-28306374	K562	blood:	n/a	chr6:28300992-28301002 chr6:28304956-28304965 chr6:28304017-28304027
20	IRF1	chr6:28302784-28305143	K562	blood:	n/a	chr6:28304586-28304595 chr6:28303699-28303713 chr6:28303781-28303795
21	POLR2A	chr6:28302878-28306282	HepG2	liver:	n/a	n/a
22	POLR2A	chr6:28302820-28305300	HepG2	liver:	n/a	n/a
23	STAT5A	chr6:28302665-28304923	K562	blood:	n/a	chr6:28303817-28303825 chr6:28303984-28303998
24	CHD1	chr6:28303073-28304864	H1-hESC	embryonic stem cell:	n/a	n/a
25	REST	chr6:28302479-28305717	H1-neurons	neurons:	n/a	n/a
26	RCOR1	chr6:28303269-28304888	GM12878	blood:	n/a	n/a
27	PML	chr6:28302587-28304920	K562	blood:	n/a	n/a
28	NR2F2	chr6:28302651-28304865	K562	blood:	n/a	n/a
29	CREB1	chr6:28303056-28304850	GM12878	blood:	n/a	n/a
30	TAL1	chr6:28302555-28305327	K562	blood:	n/a	n/a
31	SPI1	chr6:28303567-28305284	HL-60	blood:	n/a	chr6:28304590-28304597
32	POLR2A	chr6:28302776-28305339	K562	blood:	n/a	n/a
33	POLR2A	chr6:28303038-28306300	HepG2	liver:	n/a	n/a
34	GATA1	chr6:28300581-28305726	K562	blood:	n/a	chr6:28304955-28304965
35	POLR2A	chr6:28302883-28305228	K562	blood:	n/a	n/a
36	IRF1	chr6:28302141-28305143	K562	blood:	n/a	chr6:28304586-28304595 chr6:28303699-28303713 chr6:28303781-28303795
37	TEAD4	chr6:28302245-28305315	K562	blood:	n/a	n/a
38	TRIM28	chr6:28302632-28304942	K562	blood:	n/a	n/a
39	POLR2A	chr6:28302885-28305327	K562	blood:	n/a	n/a
40	MAZ	chr6:28302799-28304888	K562	blood:	n/a	n/a
41	POLR2A	chr6:28302795-28305406	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr6:28302772-28306469	K562	blood:	n/a	n/a
43	JUND	chr6:28302598-28304892	SK-N-SH	brain:	n/a	chr6:28303395-28303406 chr6:28304017-28304027
44	POLR2A	chr6:28302783-28305842	K562	blood:	n/a	n/a
45	POLR2A	chr6:28302201-28305503	H1-hESC	embryonic stem cell:	n/a	n/a
46	TBL1XR1	chr6:28302750-28304875	K562	blood:	n/a	n/a
47	POLR2A	chr6:28302830-28305370	K562	blood:	n/a	n/a
48	CREB1	chr6:28302701-28304848	K562	blood:	n/a	n/a
49	CREB1	chr6:28304186-28304846	GM12878	blood:	n/a	n/a
50	HEY1	chr6:28302935-28305298	K562	blood:	n/a	n/a

No data

(count:34 , 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	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
9	chr6:27832219..27835088-chr6:28302807..28305055,2	K562	blood:
10	chr6:28303262..28304846-chr9:91923985..91926684,2	MCF-7	breast:
11	chr6:27774293..27778194-chr6:28301096..28304976,3	K562	blood:
12	chr6:28109273..28111011-chr6:28302779..28305242,3	MCF-7	breast:
13	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
14	chr6:27798625..27800434-chr6:28302917..28305015,2	K562	blood:
15	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
16	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
17	chr6:28232839..28237434-chr6:28303380..28305726,5	MCF-7	breast:
18	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
19	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
20	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
21	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
22	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
23	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
24	chr6:28302165..28304933-chr6:28366158..28368845,2	K562	blood:
25	chr6:28126892..28131515-chr6:28301205..28304944,6	K562	blood:
26	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:
27	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
28	chr6:28287491..28290035-chr6:28302948..28305431,2	K562	blood:
29	chr6:28304462..28306809-chr6:28341388..28343447,2	K562	blood:
30	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
31	chr6:28226019..28228390-chr6:28303494..28305290,2	K562	blood:
32	chr6:27802790..27806364-chr6:28301138..28304856,3	K562	blood:
33	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
34	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000123975	Chromatin interaction
ENSG00000198374	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000270326	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000233224	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233710	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs1416919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635	0.85[CEU][hapmap]
rs16893917	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893929	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077474	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs213233	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs2159275	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299030	0.85[CEU][hapmap]
rs3800324	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800327	1.00[CEU][hapmap]
rs4711167	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713159	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58019071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59598126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60698636	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73742544	0.84[AFR][1000 genomes]
rs73742545	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs742107	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs758397	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7750106	0.85[CEU][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

No data

Chromatin state (count:114 , 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	chr6:28302400-28305200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:28302400-28305200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:28302400-28305600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28302600-28305200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28302600-28305200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:28302800-28305000	Active TSS	Colonic Mucosa	Colon
8	chr6:28302800-28305000	Active TSS	Right Atrium	heart
9	chr6:28302800-28305000	Active TSS	Right Ventricle	heart
10	chr6:28302800-28305200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:28302800-28305200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:28303000-28305000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:28303000-28305200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:28303000-28305200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:28303200-28305000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:28303200-28305000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:28303200-28305000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr6:28303200-28305000	Active TSS	Fetal Brain Male	brain
19	chr6:28303200-28305000	Active TSS	Fetal Muscle Trunk	muscle
20	chr6:28303200-28305200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr6:28303200-28305400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:28303600-28305000	Flanking Active TSS	HMEC	breast
23	chr6:28303800-28305000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr6:28303800-28305200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:28304000-28305000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:28304000-28305000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr6:28304000-28305000	Flanking Active TSS	Hela-S3	cervix
28	chr6:28304000-28305000	Flanking Active TSS	NH-A	brain
29	chr6:28304000-28305400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:28304200-28305000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:28304200-28305000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:28304200-28305000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:28304200-28305000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:28304200-28305000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:28304200-28305000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr6:28304200-28305000	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr6:28304200-28305200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr6:28304200-28305200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr6:28304200-28305200	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr6:28304200-28305200	Flanking Active TSS	Dnd41	blood
41	chr6:28304200-28305400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr6:28304400-28305000	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr6:28304400-28305000	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr6:28304400-28305000	Flanking Active TSS	Fetal Brain Female	brain
45	chr6:28304400-28305000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:28304400-28305000	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr6:28304400-28305200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:28304400-28305200	Enhancers	Spleen	Spleen
49	chr6:28304400-28305400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:28304400-28305400	Flanking Active TSS	Fetal Kidney	kidney

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