Variant report

Variant	rs877500
Chromosome Location	chr20:16248453-16248454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16241933..16245769-chr20:16247318..16250085,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11905881	1.00[CHD][hapmap]
rs17659157	1.00[CHB][hapmap]
rs17670690	1.00[CHB][hapmap]
rs1884601	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4563306	1.00[CHB][hapmap]
rs4814465	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814482	1.00[CHD][hapmap]
rs6043850	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043873	1.00[CHB][hapmap]
rs6043875	1.00[CHB][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs6075046	1.00[CHB][hapmap]
rs6080212	1.00[CHB][hapmap]
rs6080213	1.00[CHB][hapmap]
rs6080214	1.00[CHB][hapmap]
rs6080215	1.00[CHB][hapmap]
rs6080221	1.00[CHB][hapmap]
rs6080233	1.00[CHB][hapmap]
rs6111006	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111010	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[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	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv519621	chr20:16236837-16248453	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv516591	chr20:16238023-16248453	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs877500	HSPC072	cis	parietal	SCAN
rs877500	C20orf23	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16244800-16253400	Weak transcription	Ovary	ovary
3	chr20:16246600-16253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:16247200-16248600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:16247200-16248600	ZNF genes & repeats	Fetal Stomach	stomach
6	chr20:16247200-16249000	ZNF genes & repeats	Aorta	Aorta
7	chr20:16247400-16248600	Strong transcription	Stomach Smooth Muscle	stomach
8	chr20:16247400-16253600	Weak transcription	Gastric	stomach
9	chr20:16247600-16253200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr20:16247600-16290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr20:16248000-16248600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr20:16248000-16248800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr20:16248000-16248800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
14	chr20:16248000-16248800	ZNF genes & repeats	Lung	lung
15	chr20:16248000-16248800	ZNF genes & repeats	Spleen	Spleen
16	chr20:16248000-16249000	Strong transcription	Right Ventricle	heart
17	chr20:16248000-16254400	Weak transcription	Fetal Muscle Leg	muscle
18	chr20:16248200-16248600	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr20:16248200-16248600	Weak transcription	Fetal Intestine Small	intestine
20	chr20:16248200-16253400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr20:16248200-16253600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:16248200-16255400	Weak transcription	Placenta	Placenta
23	chr20:16248400-16248800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
24	chr20:16248400-16248800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr20:16248400-16259400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr20:16248400-16260800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:16248400-16261000	Weak transcription	Left Ventricle	heart
28	chr20:16248400-16263200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr20:16248400-16263800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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