Variant report

Variant	rs563342
Chromosome Location	chr3:140190809-140190810
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140185147..140188078-chr3:140189944..140194087,5	MCF-7	breast:
2	chr3:140184688..140187114-chr3:140190424..140192201,2	MCF-7	breast:
3	chr3:140188983..140190979-chr3:140192938..140195327,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs168386	0.84[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	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs524554	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]
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	0.84[CEU][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs534395	0.84[CEU][hapmap]
rs549244	0.81[EUR][1000 genomes]
rs564538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140185600-140192000	Enhancers	NHDF-Ad	bronchial
2	chr3:140185800-140192200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:140186000-140192400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:140186600-140191800	Weak transcription	HMEC	breast
5	chr3:140186600-140197800	Weak transcription	Adipose Nuclei	Adipose
6	chr3:140187000-140191200	Weak transcription	NH-A	brain
7	chr3:140187400-140193600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:140187600-140194800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:140188600-140195800	Weak transcription	Ovary	ovary
10	chr3:140188800-140191200	Weak transcription	HSMMtube	muscle
11	chr3:140189200-140191000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:140189200-140191000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:140189200-140191000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:140189400-140191400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:140189400-140192200	Enhancers	Osteobl	bone
16	chr3:140189600-140192200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:140189800-140192400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:140190000-140191400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:140190000-140192200	Enhancers	A549	lung
20	chr3:140190200-140191800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:140190400-140191000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:140190400-140191400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:140190800-140191000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:140190800-140191000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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