Variant report

Variant	rs7875945
Chromosome Location	chr9:116074212-116074213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116068586..116075781-chr9:116167998..116173640,10	MCF-7	breast:
2	chr9:116071329..116074445-chr9:116134233..116136581,3	MCF-7	breast:
3	chr9:116048493..116050036-chr9:116073858..116076574,2	K562	blood:

Variant related genes	Relation type
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10481639	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481674	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.90[YRI][hapmap]
rs10817480	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981726	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10981731	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981740	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981741	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981742	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981744	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981750	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981751	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981752	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981760	0.89[EUR][1000 genomes]
rs12006029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336832	1.00[JPT][hapmap]
rs12337552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338029	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339382	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342549	1.00[JPT][hapmap]
rs12344170	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344525	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348629	1.00[JPT][hapmap]
rs12349500	1.00[JPT][hapmap]
rs12350131	0.89[YRI][hapmap]
rs12351134	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351296	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351630	0.97[EUR][1000 genomes]
rs12352925	1.00[JPT][hapmap]
rs13440199	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932649	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17764563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17831256	1.00[JPT][hapmap]
rs28495580	0.89[EUR][1000 genomes]
rs28607343	0.89[EUR][1000 genomes]
rs3750529	1.00[CHB][hapmap]
rs3789254	1.00[CHB][hapmap]
rs41276795	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324980	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4437724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4442214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4445296	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560870	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5012573	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60528957	0.89[EUR][1000 genomes]
rs60849153	1.00[ASN][1000 genomes]
rs66649870	0.89[EUR][1000 genomes]
rs67292897	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7025347	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027445	0.97[EUR][1000 genomes]
rs7041782	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863485	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863910	1.00[JPT][hapmap]
rs7865438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];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
rs7875945	BSPRY	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 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	chr9:116062600-116075600	Weak transcription	Placenta	Placenta
4	chr9:116065400-116086800	Weak transcription	Gastric	stomach
5	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
7	chr9:116070000-116080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:116070200-116077400	Weak transcription	Ovary	ovary
9	chr9:116070200-116077800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
11	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:116072400-116074600	Enhancers	Left Ventricle	heart
13	chr9:116072800-116074600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:116072800-116079200	Weak transcription	Lung	lung
15	chr9:116072800-116080200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:116073000-116080400	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:116073200-116077200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:116073200-116077400	Weak transcription	Fetal Stomach	stomach
19	chr9:116073200-116078400	Weak transcription	Pancreas	Pancrea
20	chr9:116073200-116079600	Weak transcription	Fetal Lung	lung
21	chr9:116073200-116081000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:116073800-116076200	Enhancers	Fetal Muscle Leg	muscle
23	chr9:116073800-116080000	Weak transcription	Adipose Nuclei	Adipose
24	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:116074000-116074400	Weak transcription	Right Ventricle	heart
26	chr9:116074000-116079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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