Variant report

Variant	rs12338029
Chromosome Location	chr9:116077514-116077515
allele	C/G
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116076424..116079127-chr9:116102528..116104331,2	MCF-7	breast:
2	chr9:116071625..116073462-chr9:116076376..116079141,2	K562	blood:
3	chr9:116076058..116079132-chr9:116081074..116084162,3	K562	blood:
4	chr9:116077143..116079692-chr9:116110149..116111989,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR31-1	chr9:116076583-116077893	ENSG00000248151
2	lnc-WDR31-1	chr9:116076583-116077893	NONHSAT134340

No data

Variant related genes	Relation type
ENSG00000148225	Chromatin interaction
ENSG00000119411	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	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817480	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981726	0.95[EUR][1000 genomes]
rs10981731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981733	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981740	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981741	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981742	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981743	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981744	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981745	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981746	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981747	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981748	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981750	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981751	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981760	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12006029	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337552	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339382	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344170	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344525	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351134	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351296	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351630	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13440199	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543535	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932649	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17764563	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28495580	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28607343	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41276795	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324980	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4437724	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4442214	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445296	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560870	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636275	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012573	1.00[EUR][1000 genomes]
rs60528957	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60849153	1.00[ASN][1000 genomes]
rs66649870	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67292897	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025347	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027445	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7041782	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863485	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875945	1.00[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
rs12338029	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116065400-116086800	Weak transcription	Gastric	stomach
4	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
5	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
6	chr9:116070000-116080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:116070200-116077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
9	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:116072800-116079200	Weak transcription	Lung	lung
11	chr9:116072800-116080200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:116073000-116080400	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:116073200-116078400	Weak transcription	Pancreas	Pancrea
14	chr9:116073200-116079600	Weak transcription	Fetal Lung	lung
15	chr9:116073200-116081000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:116073800-116080000	Weak transcription	Adipose Nuclei	Adipose
17	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:116074000-116079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:116074600-116077600	Weak transcription	Brain Anterior Caudate	brain
20	chr9:116074600-116079800	Weak transcription	Left Ventricle	heart
21	chr9:116074600-116080600	Weak transcription	Right Ventricle	heart
22	chr9:116075800-116078400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:116075800-116079000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:116076000-116084600	Weak transcription	HSMMtube	muscle
25	chr9:116076200-116078400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:116076200-116081000	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:116076200-116085000	Weak transcription	Placenta	Placenta
28	chr9:116076400-116078800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:116076400-116081000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr9:116076600-116078800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:116077000-116079000	Weak transcription	Fetal Intestine Large	intestine
32	chr9:116077000-116080600	Weak transcription	Fetal Kidney	kidney
33	chr9:116077000-116086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr9:116077200-116085600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:116077400-116077600	Weak transcription	Aorta	Aorta
36	chr9:116077400-116079200	Weak transcription	Brain Hippocampus Middle	brain
37	chr9:116077400-116080600	Weak transcription	Brain Angular Gyrus	brain
38	chr9:116077400-116080600	Weak transcription	Brain Substantia Nigra	brain
39	chr9:116077400-116082800	Weak transcription	Colonic Mucosa	Colon
40	chr9:116077400-116083800	Strong transcription	Ovary	ovary
41	chr9:116077400-116084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:116077400-116084200	Strong transcription	Fetal Stomach	stomach
43	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
44	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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