Variant report

Variant	rs7860632
Chromosome Location	chr9:21683289-21683290
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21678019..21679658-chr9:21681885..21684334,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11999970	0.83[ASN][1000 genomes]
rs13287072	0.99[ASN][1000 genomes]
rs1478058	0.83[ASN][1000 genomes]
rs16938532	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16938533	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869205	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2020334	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2020344	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2039584	0.84[ASN][1000 genomes]
rs2039585	0.87[ASN][1000 genomes]
rs2039586	0.84[ASN][1000 genomes]
rs2083560	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2383200	0.83[ASN][1000 genomes]
rs2383201	0.87[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2891163	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34410759	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4147137	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41517746	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs4307419	0.83[ASN][1000 genomes]
rs4629957	0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6475544	0.83[ASN][1000 genomes]
rs67479509	0.82[ASN][1000 genomes]
rs7021741	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7028436	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7028637	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7028950	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7029077	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7035252	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7035284	0.83[ASN][1000 genomes]
rs7045371	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7852691	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7865123	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865502	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7866337	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7866521	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs921560	0.87[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][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	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015623	chr9:21579110-21694039	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv892742	chr9:21589041-21707372	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7860632	FAM154A	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21677200-21684600	Enhancers	Hela-S3	cervix
2	chr9:21678000-21688200	Enhancers	HMEC	breast
3	chr9:21678200-21684000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:21678400-21687400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:21678600-21684600	Enhancers	HUVEC	blood vessel
6	chr9:21680400-21683400	Enhancers	HSMM	muscle
7	chr9:21680400-21684200	Enhancers	NHLF	lung
8	chr9:21680400-21684600	Enhancers	NH-A	brain
9	chr9:21680400-21685000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:21680400-21686000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr9:21680400-21688200	Flanking Active TSS	A549	lung
12	chr9:21680400-21688200	Enhancers	Osteobl	bone
13	chr9:21680400-21691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:21681400-21684400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:21681600-21684400	Enhancers	Stomach Mucosa	stomach
16	chr9:21682000-21683400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:21682200-21683400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:21682200-21687800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:21682200-21688000	Enhancers	NHDF-Ad	bronchial
20	chr9:21682600-21683400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:21682800-21684000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:21683200-21683400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:21683200-21684400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:21683200-21685000	Flanking Active TSS	NHEK	skin
25	chr9:21683200-21688000	Weak transcription	Small Intestine	intestine

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