Variant report

Variant	rs3792822
Chromosome Location	chr5:40775297-40775298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:40775124-40776020	MCF-7	breast:	n/a	n/a
2	GATA3	chr5:40775024-40775955	T-47D	breast:	n/a	n/a
3	EP300	chr5:40775087-40775961	T-47D	breast:	n/a	n/a
4	ESR1	chr5:40775129-40775936	T-47D	breast:	n/a	n/a
5	ZNF217	chr5:40775227-40775741	MCF-7	breast:	n/a	n/a
6	NR2F2	chr5:40775220-40775861	MCF-7	breast:	n/a	n/a
7	FOXA2	chr5:40775156-40776021	A549	lung:	n/a	n/a
8	GATA3	chr5:40774969-40775855	MCF-7	breast:	n/a	n/a
9	TCF7L2	chr5:40775222-40775466	PANC-1	pancreas:	n/a	n/a
10	JUND	chr5:40774919-40776478	T-47D	breast:	n/a	n/a
11	ESR1	chr5:40775086-40775879	T-47D	breast:	n/a	n/a
12	FOXA1	chr5:40775118-40775897	T-47D	breast:	n/a	chr5:40775780-40775795
13	ESR1	chr5:40775121-40775787	T-47D	breast:	n/a	n/a
14	GATA3	chr5:40774757-40776579	T-47D	breast:	n/a	n/a
15	ESR1	chr5:40774978-40776003	T-47D	breast:	n/a	n/a
16	ESR1	chr5:40775038-40775956	T-47D	breast:	n/a	n/a
17	TCF12	chr5:40774887-40775726	MCF-7	breast:	n/a	n/a
18	SIN3AK20	chr5:40774987-40775852	MCF-7	breast:	n/a	n/a
19	JUND	chr5:40775059-40775887	T-47D	breast:	n/a	n/a
20	GATA3	chr5:40775240-40775751	MCF-7	breast:	n/a	n/a
21	EP300	chr5:40775027-40775928	T-47D	breast:	n/a	n/a
22	NR2F2	chr5:40775134-40775910	MCF-7	breast:	n/a	n/a
23	HDAC2	chr5:40775117-40775846	MCF-7	breast:	n/a	n/a
24	GATA3	chr5:40774929-40776056	MCF-7	breast:	n/a	n/a
25	ESR1	chr5:40775140-40775836	T-47D	breast:	n/a	n/a
26	FOXA1	chr5:40775119-40776358	T-47D	breast:	n/a	chr5:40775780-40775795
27	TCF12	chr5:40774967-40775645	A549	lung:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40774709..40775397-chr5:40797933..40799029,3	MCF-7	breast:
2	chr5:40772744..40775681-chr5:40786682..40789617,2	K562	blood:
3	chr5:40772314..40777301-chr5:40833033..40836995,8	MCF-7	breast:
4	chr5:40773952..40776932-chr5:40826531..40828937,3	MCF-7	breast:
5	chr5:40774463..40775388-chr5:40879209..40879987,4	MCF-7	breast:
6	chr5:40758950..40761144-chr5:40774547..40777219,2	MCF-7	breast:
7	chr5:40774793..40777678-chr5:40788582..40791968,3	K562	blood:
8	chr5:40773648..40776497-chr5:40822684..40825519,3	K562	blood:
9	chr5:40773991..40776066-chr5:40782651..40784458,2	K562	blood:
10	chr5:40774212..40777174-chr5:40790715..40793057,3	MCF-7	breast:
11	chr5:40773379..40776613-chr5:40796671..40799412,4	MCF-7	breast:
12	chr5:40774863..40776772-chr5:40831015..40832894,2	MCF-7	breast:
13	chr5:40774559..40777088-chr5:40796759..40799158,4	MCF-7	breast:
14	chr5:40760022..40761857-chr5:40773793..40775649,2	K562	blood:
15	chr5:40773088..40775822-chr5:40794513..40796616,2	MCF-7	breast:
16	chr5:40773990..40775613-chr5:40787064..40789947,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRKAA1	TF binding region
ENSG00000212296	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16870224	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.80[TSI][hapmap]
rs16870378	0.84[ASW][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs3805486	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];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4957341	0.94[CHB][hapmap];0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3792822	FBXO4	cis	parietal	SCAN
rs3792822	PTGER4	cis	cerebellum	SCAN
rs3792822	C7	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756000-40776000	Weak transcription	Aorta	Aorta
2	chr5:40756000-40780600	Weak transcription	Spleen	Spleen
3	chr5:40756200-40797200	Weak transcription	Gastric	stomach
4	chr5:40756400-40776200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:40756400-40776400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:40756400-40776800	Weak transcription	Psoas Muscle	Psoas
7	chr5:40756400-40780600	Weak transcription	Esophagus	oesophagus
8	chr5:40756400-40785200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:40756600-40775800	Weak transcription	Fetal Heart	heart
11	chr5:40756600-40776000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:40756600-40780600	Weak transcription	Pancreas	Pancrea
13	chr5:40756600-40781200	Weak transcription	Fetal Brain Male	brain
14	chr5:40757200-40777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:40758200-40777000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:40758400-40777800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:40759000-40776200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:40759400-40777000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:40759400-40777200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:40759600-40776000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr5:40759800-40776000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:40760000-40777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:40760400-40776200	Strong transcription	Osteobl	bone
24	chr5:40760600-40776000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:40760600-40777600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:40760800-40777600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:40761000-40775600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:40761200-40776000	Strong transcription	Liver	Liver
29	chr5:40761400-40776000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:40761400-40777600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:40761600-40777600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:40762000-40777800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr5:40762000-40778400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:40763200-40777200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:40763400-40776000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:40763600-40777600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:40765200-40775400	Weak transcription	Brain Angular Gyrus	brain
38	chr5:40765200-40775800	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:40765400-40776000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr5:40765400-40776000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:40765400-40778200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
43	chr5:40765600-40776000	Weak transcription	Thymus	Thymus
44	chr5:40765600-40776200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:40766000-40782200	Weak transcription	Brain Substantia Nigra	brain
47	chr5:40767200-40775600	Weak transcription	Small Intestine	intestine
48	chr5:40767400-40775800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:40767800-40776000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:40768400-40775600	Weak transcription	Left Ventricle	heart

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