Variant report

Variant	rs60528957
Chromosome Location	chr9:116114246-116114247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116112976..116115054-chr9:116115085..116116590,2	K562	blood:
2	chr9:116113999..116116348-chr9:116162534..116164296,2	MCF-7	breast:
3	chr9:116111218..116114895-chr9:116159419..116161993,4	MCF-7	breast:
4	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
5	chr9:116064341..116066340-chr9:116112890..116114415,2	MCF-7	breast:
6	chr9:116035712..116039392-chr9:116113201..116116002,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf43-3	chr9:116113497-116114564	expReg_chr9_6671_+

No data

Variant related genes	Relation type
ENSG00000148218	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000119431	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10481639	0.85[EUR][1000 genomes]
rs10817480	0.85[EUR][1000 genomes]
rs10981726	0.87[EUR][1000 genomes]
rs10981731	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10981733	0.89[EUR][1000 genomes]
rs10981740	0.85[EUR][1000 genomes]
rs10981741	0.85[EUR][1000 genomes]
rs10981742	0.85[EUR][1000 genomes]
rs10981743	0.85[EUR][1000 genomes]
rs10981744	0.85[EUR][1000 genomes]
rs10981745	0.85[EUR][1000 genomes]
rs10981746	0.85[EUR][1000 genomes]
rs10981747	0.85[EUR][1000 genomes]
rs10981748	0.85[EUR][1000 genomes]
rs10981750	0.84[EUR][1000 genomes]
rs10981751	0.85[EUR][1000 genomes]
rs10981752	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10981760	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006029	0.85[EUR][1000 genomes]
rs12337552	0.89[EUR][1000 genomes]
rs12338029	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12339382	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12344170	0.85[EUR][1000 genomes]
rs12344525	0.85[EUR][1000 genomes]
rs12351134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12351296	0.85[EUR][1000 genomes]
rs12351630	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13440199	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1543535	0.85[EUR][1000 genomes]
rs16932583	0.89[EUR][1000 genomes]
rs16932649	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17764563	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28495580	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607343	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750529	0.85[ASN][1000 genomes]
rs3789254	0.85[ASN][1000 genomes]
rs41276795	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4324980	0.85[EUR][1000 genomes]
rs4437724	0.85[EUR][1000 genomes]
rs4445296	0.85[EUR][1000 genomes]
rs4560870	0.84[EUR][1000 genomes]
rs4636275	0.85[EUR][1000 genomes]
rs5012573	0.89[EUR][1000 genomes]
rs60849153	0.84[EUR][1000 genomes]
rs66649870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67292897	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7025347	0.85[EUR][1000 genomes]
rs7027445	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7041782	0.85[EUR][1000 genomes]
rs73537095	0.85[AFR][1000 genomes]
rs7863485	0.85[EUR][1000 genomes]
rs7865438	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7875945	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60528957	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116112800-116115400	Enhancers	Stomach Mucosa	stomach
2	chr9:116112800-116122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:116113000-116135600	Weak transcription	Colonic Mucosa	Colon
4	chr9:116113000-116138000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:116113200-116117000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:116113400-116114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:116113400-116114600	Weak transcription	Esophagus	oesophagus
8	chr9:116113400-116116400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:116113400-116135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:116113600-116114600	Weak transcription	Gastric	stomach
11	chr9:116113600-116115200	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:116113800-116115200	Enhancers	GM12878-XiMat	blood
13	chr9:116113800-116115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:116113800-116122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:116113800-116137800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr9:116114000-116114800	Weak transcription	Pancreas	Pancrea
17	chr9:116114000-116115200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr9:116114000-116115200	Enhancers	HepG2	liver
19	chr9:116114000-116115600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:116114000-116127400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:116114200-116136400	Weak transcription	Primary B cells from cord blood	blood

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