Variant report

Variant	rs524554
Chromosome Location	chr3:140189148-140189149
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	chr3:140188983..140190979-chr3:140192938..140195327,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs168386	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs349504	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs349507	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs349510	0.80[EUR][1000 genomes]
rs349511	0.80[EUR][1000 genomes]
rs349536	0.81[CHB][hapmap]
rs349542	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs472412	0.82[EUR][1000 genomes]
rs503088	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505853	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530046	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs531617	0.85[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs534395	0.84[CEU][hapmap]
rs549244	0.81[EUR][1000 genomes]
rs563342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564538	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1004500	chr3:140021594-140189148	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140185600-140192000	Enhancers	NHDF-Ad	bronchial
2	chr3:140185800-140190400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:140185800-140192200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:140186000-140192400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:140186600-140189200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:140186600-140191800	Weak transcription	HMEC	breast
7	chr3:140186600-140197800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:140187000-140190000	Weak transcription	A549	lung
9	chr3:140187000-140191200	Weak transcription	NH-A	brain
10	chr3:140187200-140189600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:140187400-140189400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:140187400-140193600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:140187600-140189600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:140187600-140189600	Weak transcription	HSMM	muscle
15	chr3:140187600-140194800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:140188000-140189600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:140188200-140189400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:140188200-140189800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:140188200-140190000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr3:140188200-140190200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:140188400-140190400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
22	chr3:140188600-140189800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:140188600-140190200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:140188600-140195800	Weak transcription	Ovary	ovary
25	chr3:140188800-140189800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:140188800-140191200	Weak transcription	HSMMtube	muscle
27	chr3:140189000-140189200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:140189000-140189200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr3:140189000-140189400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:140189000-140189400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:140189000-140189400	Weak transcription	Osteobl	bone

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