Variant report

Variant	rs2087550
Chromosome Location	chr1:151934983-151934984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151919533..151922319-chr1:151932817..151935606,2	MCF-7	breast:
2	chr1:151933684..151936159-chr1:151941486..151943210,2	MCF-7	breast:
3	chr1:151932606..151935514-chr1:151936511..151938848,2	MCF-7	breast:
4	chr1:151913842..151916280-chr1:151933238..151936084,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1038746	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1038748	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387834	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387835	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473493	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473494	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473495	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490190	0.82[AMR][1000 genomes]
rs1490191	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1532132	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552605	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552607	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602245	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1602246	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602248	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17583707	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1826170	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1826171	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1826172	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1844542	0.85[AMR][1000 genomes]
rs1873311	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2338018	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2338210	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932563	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932564	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932578	0.82[AMR][1000 genomes]
rs2932584	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932585	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932588	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932591	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932592	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932595	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932596	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999511	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999514	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999515	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999518	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999519	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999520	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999522	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999523	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999524	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999525	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999527	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999529	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999530	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999558	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3007682	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3007692	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3007693	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3007699	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007700	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007701	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3007704	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34370890	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61113720	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6587630	0.82[ASN][1000 genomes]
rs6678664	0.82[ASN][1000 genomes]
rs971888	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2087550	VPS72	cis	Stomach	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151930800-151940800	Weak transcription	NHDF-Ad	bronchial
2	chr1:151931800-151935200	Weak transcription	Hela-S3	cervix
3	chr1:151932800-151936400	Enhancers	Fetal Kidney	kidney
4	chr1:151933200-151936200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:151933400-151935600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:151933400-151936400	Enhancers	NHEK	skin
7	chr1:151933600-151937200	Enhancers	HUVEC	blood vessel
8	chr1:151933600-151945000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:151934000-151940600	Weak transcription	Gastric	stomach
10	chr1:151934200-151935400	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:151934200-151935800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:151934200-151936800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:151934200-151937000	Weak transcription	Stomach Mucosa	stomach
14	chr1:151934200-151940600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:151934200-151942600	Weak transcription	HSMM	muscle
16	chr1:151934400-151940200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr1:151934600-151936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:151934600-151940600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
20	chr1:151934800-151935200	Enhancers	Fetal Muscle Trunk	muscle
21	chr1:151934800-151935200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:151934800-151936800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:151934800-151939600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:151934800-151940200	Weak transcription	Fetal Intestine Large	intestine

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