Variant report

Variant	rs4445296
Chromosome Location	chr9:116109053-116109054
allele	C/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	GATA3	chr9:116108699-116109065	T-47D	breast:	n/a	chr9:116108957-116108965
2	GATA2	chr9:116108764-116109072	SH-SY5Y	brain:	n/a	chr9:116108957-116108965
3	EP300	chr9:116108550-116109342	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr9:116108758-116109127	MCF-7	breast:	n/a	chr9:116108957-116108965

No.	Distal block	Cell Line	Cell type
1	chr9:116106104..116109704-chr9:116111339..116114258,3	K562	blood:
2	chr9:116108733..116111186-chr9:116118329..116120582,2	MCF-7	breast:
3	chr9:116108849..116110601-chr9:116170239..116173217,2	K562	blood:
4	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
5	chr9:116038056..116040048-chr9:116108621..116111534,2	MCF-7	breast:

Variant related genes	Relation type
BSPRY	TF binding region
ENSG00000119411	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10481639	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817480	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981726	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10981731	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981733	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981740	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981741	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981742	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981743	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981744	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981745	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981746	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981747	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981748	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981751	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981752	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981760	0.85[EUR][1000 genomes]
rs12006029	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337552	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338029	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339382	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344170	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344525	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351134	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351296	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351630	0.93[EUR][1000 genomes]
rs13440199	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543535	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932583	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932649	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17764563	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28495580	0.85[EUR][1000 genomes]
rs28607343	0.85[EUR][1000 genomes]
rs41276795	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324980	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4437724	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4442214	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636275	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012573	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60528957	0.85[EUR][1000 genomes]
rs60849153	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66649870	0.85[EUR][1000 genomes]
rs67292897	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025347	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027445	0.93[EUR][1000 genomes]
rs7041782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863485	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865438	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875945	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4445296	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116103000-116111800	Weak transcription	Lung	lung
2	chr9:116103200-116110000	Weak transcription	Right Atrium	heart
3	chr9:116103200-116111400	Weak transcription	Stomach Mucosa	stomach
4	chr9:116103200-116111400	Weak transcription	GM12878-XiMat	blood
5	chr9:116105800-116110200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr9:116105800-116111400	Enhancers	Fetal Intestine Small	intestine
7	chr9:116105800-116111400	Weak transcription	Right Ventricle	heart
8	chr9:116106200-116111400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:116106400-116109200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:116106400-116110400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:116106600-116109400	Weak transcription	Colonic Mucosa	Colon
12	chr9:116106600-116110000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:116106600-116111400	Weak transcription	Liver	Liver
14	chr9:116106600-116111400	Weak transcription	Esophagus	oesophagus
15	chr9:116106600-116111400	Weak transcription	Pancreas	Pancrea
16	chr9:116106600-116111800	Weak transcription	K562	blood
17	chr9:116107600-116111600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:116107800-116110000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:116107800-116110000	Weak transcription	Small Intestine	intestine
20	chr9:116107800-116111200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr9:116108000-116110000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:116108000-116110000	Weak transcription	Fetal Heart	heart
23	chr9:116108000-116111400	Weak transcription	Brain Anterior Caudate	brain
24	chr9:116108000-116111600	Weak transcription	Brain Angular Gyrus	brain
25	chr9:116108000-116112000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:116108200-116109600	Weak transcription	Fetal Intestine Large	intestine
27	chr9:116108200-116109600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:116108200-116111200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:116108200-116112000	Weak transcription	Brain Substantia Nigra	brain
30	chr9:116108600-116109800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:116108600-116111400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:116108800-116111400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:116108800-116111400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr9:116108800-116111800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:116109000-116110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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