Variant report

Variant	rs73742539
Chromosome Location	chr6:28305471-28305472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:28302119-28305609	K562	blood:	n/a	n/a
2	JUN	chr6:28300330-28306374	K562	blood:	n/a	chr6:28300992-28301002 chr6:28304956-28304965 chr6:28304017-28304027
3	POLR2A	chr6:28302878-28306282	HepG2	liver:	n/a	n/a
4	REST	chr6:28302479-28305717	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr6:28303038-28306300	HepG2	liver:	n/a	n/a
6	GATA1	chr6:28300581-28305726	K562	blood:	n/a	chr6:28304955-28304965
7	POLR2A	chr6:28302772-28306469	K562	blood:	n/a	n/a
8	POLR2A	chr6:28302783-28305842	K562	blood:	n/a	n/a
9	POLR2A	chr6:28302201-28305503	H1-hESC	embryonic stem cell:	n/a	n/a
10	NR2F2	chr6:28302362-28305837	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28305023..28307714-chr6:28355958..28358291,2	K562	blood:
2	chr6:28191649..28195458-chr6:28301378..28307708,9	K562	blood:
3	chr6:28099723..28110178-chr6:28301599..28306918,14	K562	blood:
4	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
5	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
6	chr6:28302870..28305047-chr6:28305335..28307557,3	MCF-7	breast:
7	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
8	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
9	chr6:28232839..28237434-chr6:28303380..28305726,5	MCF-7	breast:
10	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
11	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
12	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
13	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
14	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
15	chr6:28304462..28306809-chr6:28341388..28343447,2	K562	blood:
16	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
17	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000137338	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10484542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1416919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893917	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	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893975	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]
rs2159275	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]
rs3800324	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711167	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713159	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]
rs723475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723476	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]
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	0.89[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]

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:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28302400-28305600	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr6:28304400-28317400	Weak transcription	Pancreas	Pancrea
3	chr6:28304600-28305800	Flanking Active TSS	K562	blood
4	chr6:28304800-28317200	Weak transcription	Aorta	Aorta
5	chr6:28305000-28305600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:28305000-28305600	Enhancers	Brain Cingulate Gyrus	brain
7	chr6:28305000-28305600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:28305000-28305800	Enhancers	Fetal Intestine Small	intestine
9	chr6:28305000-28306200	Enhancers	Primary hematopoietic stem cells	blood
10	chr6:28305000-28310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:28305000-28317200	Weak transcription	Brain Anterior Caudate	brain
12	chr6:28305000-28317200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:28305200-28305600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:28305200-28305600	Enhancers	Colon Smooth Muscle	Colon
15	chr6:28305200-28305600	Enhancers	HepG2	liver
16	chr6:28305200-28305800	Enhancers	Stomach Smooth Muscle	stomach
17	chr6:28305200-28308000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:28305200-28308000	Weak transcription	Fetal Stomach	stomach
19	chr6:28305200-28311800	Weak transcription	Brain Angular Gyrus	brain
20	chr6:28305200-28313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:28305200-28317000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:28305200-28317000	Weak transcription	NHEK	skin
23	chr6:28305200-28317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:28305200-28317200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:28305200-28317200	Weak transcription	HSMMtube	muscle
26	chr6:28305400-28305600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:28305400-28305600	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr6:28305400-28305600	Enhancers	Fetal Heart	heart
29	chr6:28305400-28305600	Enhancers	Fetal Kidney	kidney
30	chr6:28305400-28306200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr6:28305400-28306800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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