Variant report

Variant	rs752757
Chromosome Location	chr9:116122954-116122955
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116122597..116124839-chr9:116128759..116130936,3	MCF-7	breast:
2	chr9:116110132..116116489-chr9:116119507..116125005,8	MCF-7	breast:
3	chr9:116116084..116117603-chr9:116121725..116123605,2	MCF-7	breast:
4	chr9:116122073..116125346-chr9:116133766..116136866,3	MCF-7	breast:
5	chr9:116116293..116119291-chr9:116122385..116124255,2	K562	blood:

Variant related genes	Relation type
ENSG00000119411	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10119823	0.93[EUR][1000 genomes]
rs12352548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3763667	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4978539	0.91[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4979239	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4979241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6478009	0.80[GIH][hapmap]
rs67452982	0.95[EUR][1000 genomes]
rs7031584	0.95[EUR][1000 genomes]
rs7037201	0.80[GIH][hapmap]
rs7045908	0.99[ASN][1000 genomes]
rs752758	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7873616	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv519849	chr9:116111407-116144973	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1036586	chr9:116118902-116136993	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs752757	BSPRY	Cis_1M	lymphoblastoid	RTeQTL
rs752757	POLE3	cis	cerebellum	SCAN
rs752757	HSDL2	cis	thalamus	BrainEAC
rs752757	IKBKAP	cis	cerebellum	SCAN
rs752757	PAIP2B	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116113000-116135600	Weak transcription	Colonic Mucosa	Colon
2	chr9:116113000-116138000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:116113400-116135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:116113800-116137800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:116114000-116127400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:116114200-116136400	Weak transcription	Primary B cells from cord blood	blood
7	chr9:116115400-116123400	Weak transcription	Stomach Mucosa	stomach
8	chr9:116115400-116135000	Weak transcription	Esophagus	oesophagus
9	chr9:116115600-116132800	Weak transcription	Fetal Intestine Large	intestine
10	chr9:116115800-116125800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:116116400-116137000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:116116600-116126400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:116117800-116124000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:116120200-116126400	Strong transcription	Fetal Intestine Small	intestine
15	chr9:116120200-116131800	Weak transcription	Lung	lung
16	chr9:116120400-116127200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr9:116121000-116124800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:116121600-116126400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr9:116121800-116124400	Enhancers	Pancreas	Pancrea
20	chr9:116122200-116124000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:116122400-116123200	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr9:116122400-116124000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr9:116122600-116124800	Enhancers	Brain Anterior Caudate	brain
24	chr9:116122800-116123000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:116122800-116123200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr9:116122800-116123200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:116122800-116123200	Genic enhancers	Gastric	stomach

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