Variant report

Variant	rs11921827
Chromosome Location	chr3:159355918-159355919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159351342..159356372-chr3:159480280..159483892,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10154893	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs11921824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107648	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs13434009	0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1343824	0.84[ASN][1000 genomes]
rs1347671	0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1347672	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1356926	0.81[JPT][hapmap]
rs1356927	0.85[JPT][hapmap]
rs1437519	0.83[JPT][hapmap]
rs1437520	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs1581342	0.86[JPT][hapmap]
rs16830484	0.81[JPT][hapmap]
rs16830510	0.86[JPT][hapmap]
rs16830519	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs16830523	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs16830534	0.85[ASN][1000 genomes]
rs16830546	0.89[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs16830575	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830581	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830589	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1816621	0.81[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs1816622	0.89[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962890	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1978830	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1978831	0.81[JPT][hapmap]
rs2118321	0.81[JPT][hapmap]
rs28434644	0.99[ASN][1000 genomes]
rs28743043	0.83[ASN][1000 genomes]
rs2886621	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4494974	0.90[ASN][1000 genomes]
rs59556163	0.84[ASN][1000 genomes]
rs61018732	0.84[ASN][1000 genomes]
rs61373569	0.84[ASN][1000 genomes]
rs6769217	0.81[JPT][hapmap]
rs6772245	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6796636	0.81[JPT][hapmap]
rs73012253	0.85[ASN][1000 genomes]
rs750688	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625882	0.81[JPT][hapmap]
rs7636120	0.81[JPT][hapmap]
rs7650974	0.81[JPT][hapmap]
rs9290046	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9290047	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809681	0.86[JPT][hapmap]
rs9817830	0.81[JPT][hapmap]
rs9819000	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9819080	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9824363	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs9826417	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9829310	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9832970	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9833713	0.86[JPT][hapmap]
rs9833762	0.81[JPT][hapmap]
rs9840484	0.81[JPT][hapmap]
rs9842465	0.88[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848763	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9848897	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9849705	0.82[ASN][1000 genomes]
rs9851700	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860690	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs9867212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870872	0.85[ASN][1000 genomes]
rs9877425	1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9879792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881499	0.81[JPT][hapmap]
rs9881603	0.83[JPT][hapmap]
rs9882328	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9882993	0.81[JPT][hapmap]
rs9883498	0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159350600-159358200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:159353000-159358000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:159353200-159356000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:159353200-159356200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:159353200-159358000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:159353200-159358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:159353200-159358000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:159353200-159358200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:159354800-159356200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:159354800-159356400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:159354800-159356400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:159354800-159356400	Enhancers	NHDF-Ad	bronchial
13	chr3:159355000-159356200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:159355000-159356200	Enhancers	HSMMtube	muscle
15	chr3:159355000-159356400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:159355000-159356400	Enhancers	Osteobl	bone
17	chr3:159355200-159356000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:159355200-159356400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:159355200-159356400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:159355200-159356400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:159355200-159356400	Flanking Active TSS	A549	lung
22	chr3:159355200-159356400	Enhancers	Hela-S3	cervix
23	chr3:159355200-159356400	Enhancers	HSMM	muscle
24	chr3:159355200-159356400	Enhancers	NH-A	brain
25	chr3:159355200-159356400	Enhancers	NHLF	lung
26	chr3:159355600-159356200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:159355600-159356400	Enhancers	NHEK	skin
28	chr3:159355800-159356400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:159355800-159356600	Enhancers	HMEC	breast

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