Variant report

Variant	rs3814566
Chromosome Location	chr10:45464035-45464036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr10:45463135-45464520	GM18951	blood:	n/a	n/a
2	POLR2A	chr10:45457577-45464667	GM12878	blood:	n/a	n/a
3	REST	chr10:45463166-45464849	HL-60	blood:	n/a	chr10:45463832-45463842
4	CHD2	chr10:45463267-45464549	GM12878	blood:	n/a	n/a
5	RELA	chr10:45463133-45464058	GM19099	blood:	n/a	n/a
6	SPI1	chr10:45462969-45464111	HL-60	blood:	n/a	chr10:45463769-45463778 chr10:45463708-45463717 chr10:45463706-45463719
7	RELA	chr10:45463068-45464777	GM12891	blood:	n/a	n/a
8	CEBPB	chr10:45463643-45464116	HepG2	liver:	n/a	n/a
9	EP300	chr10:45463353-45464492	GM12878	blood:	n/a	n/a
10	CEBPB	chr10:45463839-45464076	K562	blood:	n/a	n/a
11	EP300	chr10:45463184-45464675	GM12878	blood:	n/a	n/a
12	POLR2A	chr10:45463111-45464849	NB4	blood:	n/a	n/a
13	POLR2A	chr10:45462482-45464971	HL-60	blood:	n/a	n/a
14	POLR2A	chr10:45458224-45466240	HepG2	liver:	n/a	n/a
15	CEBPB	chr10:45463674-45464154	IMR90	lung:	n/a	n/a
16	POLR2A	chr10:45462972-45464974	HL-60	blood:	n/a	n/a
17	SPI1	chr10:45463219-45464195	GM12878	blood:	n/a	chr10:45463769-45463778 chr10:45463708-45463717 chr10:45463706-45463719
18	EBF1	chr10:45463059-45464044	GM12878	blood:	n/a	chr10:45463239-45463250
19	WRNIP1	chr10:45463310-45464156	GM12878	blood:	n/a	n/a
20	PML	chr10:45463754-45464523	GM12878	blood:	n/a	n/a
21	USF2	chr10:45463820-45464050	GM12878	blood:	n/a	n/a
22	MYC	chr10:45463111-45465015	NB4	blood:	n/a	chr10:45464825-45464832
23	MAX	chr10:45462487-45464904	NB4	blood:	n/a	chr10:45464825-45464832
24	BHLHE40	chr10:45463946-45464581	GM12878	blood:	n/a	n/a
25	MTA3	chr10:45463420-45464700	GM12878	blood:	n/a	n/a
26	MAX	chr10:45463974-45464680	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:45463003..45464731-chr10:45465412..45467075,2	MCF-7	breast:
2	chr10:45462150..45464959-chr10:45472680..45475248,4	MCF-7	breast:
3	chr10:45461482..45464427-chr10:45495628..45497764,2	K562	blood:

Variant related genes	Relation type
RASSF4	TF binding region
ENSG00000165511	Chromatin interaction
ENSG00000165512	Chromatin interaction
ENSG00000165507	Chromatin interaction
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10793572	0.92[ASN][1000 genomes]
rs10793573	0.96[EUR][1000 genomes]
rs12263146	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs1888983	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3829908	1.00[ASW][hapmap];0.95[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4948938	0.90[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59626742	0.81[ASN][1000 genomes]
rs7914175	0.92[ASN][1000 genomes]
rs883734	0.85[CEU][hapmap]
rs884879	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1035235	chr10:45442303-45467948	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526734	chr10:45458485-45492054	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3814566	GDF2	cis	cerebellum	SCAN
rs3814566	HNRNPF	cis	cerebellum	SCAN
rs3814566	ENSG00000107551	cis	multi-tissue	Pritchard
rs3814566	RASSF4	cis	multi-tissue	Pritchard
rs3814566	ZNF32	cis	parietal	SCAN
rs3814566	GPRIN2	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45455600-45465200	Enhancers	Fetal Thymus	thymus
2	chr10:45455600-45465200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr10:45455800-45465600	Weak transcription	Ovary	ovary
4	chr10:45456200-45465000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:45456400-45466200	Weak transcription	Aorta	Aorta
6	chr10:45456800-45465200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr10:45456800-45466600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:45458000-45465000	Enhancers	Primary B cells from cord blood	blood
9	chr10:45458200-45465000	Enhancers	Thymus	Thymus
10	chr10:45458400-45464200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr10:45458400-45464400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:45458400-45464800	Enhancers	Primary B cells from peripheral blood	blood
13	chr10:45458400-45465800	Enhancers	Psoas Muscle	Psoas
14	chr10:45458800-45465200	Enhancers	Spleen	Spleen
15	chr10:45459000-45464400	Enhancers	Placenta	Placenta
16	chr10:45459000-45465600	Enhancers	Left Ventricle	heart
17	chr10:45459800-45465200	Enhancers	Right Ventricle	heart
18	chr10:45459800-45465800	Enhancers	Right Atrium	heart
19	chr10:45460000-45470000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:45460400-45464400	Weak transcription	Fetal Brain Male	brain
21	chr10:45460400-45464600	Enhancers	Fetal Muscle Trunk	muscle
22	chr10:45460400-45469800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:45460600-45466200	Weak transcription	Fetal Brain Female	brain
24	chr10:45460800-45464200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:45460800-45464800	Enhancers	Fetal Heart	heart
26	chr10:45460800-45465400	Enhancers	Primary hematopoietic stem cells	blood
27	chr10:45461000-45464200	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr10:45461200-45464400	Enhancers	HSMM	muscle
29	chr10:45461200-45464600	Enhancers	Colon Smooth Muscle	Colon
30	chr10:45461200-45466000	Enhancers	Primary T cells fromperipheralblood	blood
31	chr10:45461200-45468200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr10:45461400-45464400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr10:45461400-45464400	Enhancers	Brain Cingulate Gyrus	brain
34	chr10:45461400-45467000	Weak transcription	Brain Germinal Matrix	brain
35	chr10:45461400-45468400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr10:45461400-45468600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr10:45461400-45468800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr10:45461600-45464200	Enhancers	Lung	lung
39	chr10:45461600-45468400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr10:45461600-45468600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:45461800-45464200	Enhancers	Stomach Mucosa	stomach
42	chr10:45461800-45466200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:45462000-45464400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:45462000-45464400	Enhancers	Stomach Smooth Muscle	stomach
45	chr10:45462000-45464800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:45462000-45465400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr10:45462000-45465600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr10:45462000-45468400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr10:45462000-45469800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:45462200-45465200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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