Variant report

Variant	rs723476
Chromosome Location	chr6:28305104-28305105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

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	YY1	chr6:28305020-28305285	K562	blood:	n/a	n/a
3	EP300	chr6:28302761-28305309	K562	blood:	n/a	n/a
4	POLR2A	chr6:28302740-28305408	K562	blood:	n/a	n/a
5	POLR2A	chr6:28302926-28305211	GM12891	blood:	n/a	n/a
6	RFX5	chr6:28302436-28305318	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:28302881-28305223	K562	blood:	n/a	n/a
8	PML	chr6:28302267-28305304	K562	blood:	n/a	n/a
9	POLR2A	chr6:28303046-28305232	GM12878	blood:	n/a	n/a
10	TEAD4	chr6:28302119-28305609	K562	blood:	n/a	n/a
11	TBL1XR1	chr6:28302835-28305371	K562	blood:	n/a	n/a
12	JUN	chr6:28300330-28306374	K562	blood:	n/a	chr6:28300992-28301002 chr6:28304956-28304965 chr6:28304017-28304027
13	IRF1	chr6:28302784-28305143	K562	blood:	n/a	chr6:28304586-28304595 chr6:28303699-28303713 chr6:28303781-28303795
14	POLR2A	chr6:28302878-28306282	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:28302820-28305300	HepG2	liver:	n/a	n/a
16	REST	chr6:28302479-28305717	H1-neurons	neurons:	n/a	n/a
17	TAL1	chr6:28302555-28305327	K562	blood:	n/a	n/a
18	SPI1	chr6:28303567-28305284	HL-60	blood:	n/a	chr6:28304590-28304597
19	POLR2A	chr6:28302776-28305339	K562	blood:	n/a	n/a
20	POLR2A	chr6:28303038-28306300	HepG2	liver:	n/a	n/a
21	GATA1	chr6:28300581-28305726	K562	blood:	n/a	chr6:28304955-28304965
22	POLR2A	chr6:28302883-28305228	K562	blood:	n/a	n/a
23	IRF1	chr6:28302141-28305143	K562	blood:	n/a	chr6:28304586-28304595 chr6:28303699-28303713 chr6:28303781-28303795
24	TEAD4	chr6:28302245-28305315	K562	blood:	n/a	n/a
25	POLR2A	chr6:28302885-28305327	K562	blood:	n/a	n/a
26	MYC	chr6:28304958-28305335	K562	blood:	n/a	chr6:28305069-28305079
27	POLR2A	chr6:28302795-28305406	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr6:28302772-28306469	K562	blood:	n/a	n/a
29	HMGN3	chr6:28304924-28305210	K562	blood:	n/a	n/a
30	POLR2A	chr6:28302783-28305842	K562	blood:	n/a	n/a
31	POLR2A	chr6:28302201-28305503	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:28302830-28305370	K562	blood:	n/a	n/a
33	KAP1	chr6:28304946-28305160	K562	blood:	n/a	n/a
34	HEY1	chr6:28302935-28305298	K562	blood:	n/a	n/a
35	TAF1	chr6:28303067-28305405	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr6:28302571-28305380	K562	blood:	n/a	n/a
37	POLR2A	chr6:28302601-28305232	K562	blood:	n/a	n/a
38	POLR2A	chr6:28302660-28305216	HL-60	blood:	n/a	n/a
39	SPI1	chr6:28304880-28305160	GM12891	blood:	n/a	n/a
40	POLR2A	chr6:28302703-28305437	H1-neurons	neurons:	n/a	n/a
41	HEY1	chr6:28302946-28305392	K562	blood:	n/a	n/a
42	SPI1	chr6:28304843-28305133	K562	blood:	n/a	n/a
43	SPI1	chr6:28304820-28305186	HL-60	blood:	n/a	n/a
44	NR2F2	chr6:28302362-28305837	K562	blood:	n/a	n/a
45	POLR2A	chr6:28302798-28305227	PBDE	blood:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28109265..28112090-chr6:28302311..28305142,2	MCF-7	breast:
2	chr6:28305023..28307714-chr6:28355958..28358291,2	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	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
7	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
8	chr6:28109273..28111011-chr6:28302779..28305242,3	MCF-7	breast:
9	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
10	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
11	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
12	chr6:28232839..28237434-chr6:28303380..28305726,5	MCF-7	breast:
13	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
14	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
15	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
16	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
17	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
18	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
19	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:
20	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
21	chr6:28287491..28290035-chr6:28302948..28305431,2	K562	blood:
22	chr6:28304462..28306809-chr6:28341388..28343447,2	K562	blood:
23	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
24	chr6:28226019..28228390-chr6:28303494..28305290,2	K562	blood:
25	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
26	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000187626	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000270326	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000235109	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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893929	0.93[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077474	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281040	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281041	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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];0.93[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];0.88[AMR][1000 genomes];0.93[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];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58019071	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59598126	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568488	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60698636	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723475	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	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742536	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742539	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742541	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73742544	0.82[AFR][1000 genomes]
rs73742545	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[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];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs758397	0.88[AMR][1000 genomes];0.95[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:90 , 50 per page) page: 1 2

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	chr6:28302800-28305200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:28302800-28305200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:28303000-28305200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:28303000-28305200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:28303200-28305200	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr6:28303200-28305400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:28303800-28305200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:28304000-28305400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:28304200-28305200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr6:28304200-28305200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr6:28304200-28305200	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr6:28304200-28305200	Flanking Active TSS	Dnd41	blood
19	chr6:28304200-28305400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:28304400-28305200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:28304400-28305200	Enhancers	Spleen	Spleen
22	chr6:28304400-28305400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:28304400-28305400	Flanking Active TSS	Fetal Kidney	kidney
24	chr6:28304400-28305400	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr6:28304400-28317400	Weak transcription	Pancreas	Pancrea
26	chr6:28304600-28305200	Enhancers	Primary B cells from peripheral blood	blood
27	chr6:28304600-28305200	Flanking Active TSS	Fetal Lung	lung
28	chr6:28304600-28305200	Enhancers	Fetal Thymus	thymus
29	chr6:28304600-28305200	Enhancers	Psoas Muscle	Psoas
30	chr6:28304600-28305400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:28304600-28305400	Flanking Active TSS	Fetal Heart	heart
32	chr6:28304600-28305400	Flanking Active TSS	GM12878-XiMat	blood
33	chr6:28304600-28305800	Flanking Active TSS	K562	blood
34	chr6:28304800-28305200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:28304800-28305200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:28304800-28305200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr6:28304800-28305200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:28304800-28305200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr6:28304800-28305200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:28304800-28305200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr6:28304800-28305200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr6:28304800-28305200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:28304800-28305200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:28304800-28305200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:28304800-28305200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:28304800-28305200	Enhancers	Brain Angular Gyrus	brain
47	chr6:28304800-28305200	Enhancers	Brain Hippocampus Middle	brain
48	chr6:28304800-28305200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:28304800-28305200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:28304800-28305200	Enhancers	Left Ventricle	heart

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