Variant report

Variant	rs41276795
Chromosome Location	chr9:116102488-116102489
allele	A/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:21998505..21999349-chr9:116102446..116103218,2	Hela-S3	cervix:
2	chr9:116100085..116103833-chr9:116137751..116140667,4	MCF-7	breast:
3	chr9:116065580..116067565-chr9:116101050..116102835,2	MCF-7	breast:
4	chr9:116099899..116105558-chr9:116170913..116174361,7	MCF-7	breast:
5	chr9:116101037..116103011-chr9:116343010..116344663,2	MCF-7	breast:
6	chr9:116063977..116066911-chr9:116102342..116104616,4	MCF-7	breast:
7	chr9:116063284..116065510-chr9:116102338..116105750,4	MCF-7	breast:
8	chr9:116101294..116104058-chr9:116110419..116112658,2	K562	blood:
9	chr9:116102456..116104363-chr9:116171276..116174227,4	MCF-7	breast:
10	chr9:116036149..116038435-chr9:116101107..116104521,3	K562	blood:
11	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168476	Chromatin interaction
ENSG00000119431	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000119411	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000176386	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	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817480	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981726	0.92[EUR][1000 genomes]
rs10981731	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981733	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981741	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981742	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981743	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981744	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981745	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981746	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981747	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981748	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981750	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981751	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981752	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981760	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12006029	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337552	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338029	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339382	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344170	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344525	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351134	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351296	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351630	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13440199	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543535	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932583	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932649	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17764563	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28495580	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28607343	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4324980	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4437724	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4442214	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445296	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560870	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636275	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012573	0.97[EUR][1000 genomes]
rs60528957	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60849153	1.00[ASN][1000 genomes]
rs66649870	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67292897	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025347	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027445	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7041782	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863485	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865438	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875945	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
rs41276795	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116101400-116102800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr9:116101400-116103000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:116101400-116103200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:116101600-116102800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:116101600-116102800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:116101600-116103000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr9:116101600-116103200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr9:116101600-116103200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:116101600-116103200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:116101600-116103200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr9:116101600-116103200	Active TSS	Brain Angular Gyrus	brain
12	chr9:116101600-116103200	Active TSS	Colonic Mucosa	Colon
13	chr9:116101600-116103200	Active TSS	Fetal Kidney	kidney
14	chr9:116101600-116103200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr9:116101600-116103200	Active TSS	Right Atrium	heart
16	chr9:116101600-116103200	Active TSS	GM12878-XiMat	blood
17	chr9:116101800-116102600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:116101800-116102600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr9:116101800-116102800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:116101800-116103000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:116101800-116103000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr9:116101800-116103000	Active TSS	Primary T cells from cord blood	blood
23	chr9:116101800-116103000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:116101800-116103000	Active TSS	Lung	lung
25	chr9:116101800-116103000	Active TSS	Right Ventricle	heart
26	chr9:116101800-116103000	Active TSS	HepG2	liver
27	chr9:116101800-116103200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:116101800-116103200	Active TSS	H9 Cell Line	embryonic stem cell
29	chr9:116101800-116103200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:116101800-116103200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:116101800-116103200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:116101800-116103200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:116101800-116103200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr9:116101800-116103200	Flanking Active TSS	Liver	Liver
35	chr9:116101800-116103200	Active TSS	Psoas Muscle	Psoas
36	chr9:116101800-116103200	Active TSS	A549	lung
37	chr9:116101800-116103200	Active TSS	NH-A	brain
38	chr9:116102000-116102600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:116102000-116102600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr9:116102000-116102600	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr9:116102000-116102800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr9:116102000-116102800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:116102000-116102800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr9:116102000-116102800	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr9:116102000-116102800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr9:116102000-116102800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr9:116102000-116102800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:116102000-116102800	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr9:116102000-116102800	Active TSS	Adipose Nuclei	Adipose
50	chr9:116102000-116102800	Active TSS	Brain Cingulate Gyrus	brain

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