Variant report

Variant	rs1561841
Chromosome Location	chr4:100380288-100380289
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	chr4:100008427..100010318-chr4:100377413..100380370,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197894	Chromatin interaction
ENSG00000246090	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1126223	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1154456	0.92[ASN][1000 genomes]
rs1154457	0.90[ASN][1000 genomes]
rs1154459	0.93[ASN][1000 genomes]
rs1154461	0.94[ASN][1000 genomes]
rs1154462	0.91[ASN][1000 genomes]
rs1154468	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1154469	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1154470	0.95[ASN][1000 genomes]
rs1154472	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1154474	0.96[ASN][1000 genomes]
rs1154475	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1154476	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1154477	0.97[ASN][1000 genomes]
rs1154480	0.99[ASN][1000 genomes]
rs1154482	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1154483	0.99[ASN][1000 genomes]
rs1154487	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1229794	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1229795	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1229796	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1910476	0.94[ASN][1000 genomes]
rs2119888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2584446	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2654846	0.83[ASN][1000 genomes]
rs2851026	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2851027	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs749406	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs749407	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv1847619	chr4:100321443-100430924	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3584519	chr4:100323870-100477462	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv3584520	chr4:100324071-100400696	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100378600-100381000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:100378800-100380400	Enhancers	Stomach Mucosa	stomach
3	chr4:100378800-100381000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:100379000-100380400	Weak transcription	Esophagus	oesophagus
5	chr4:100379400-100381000	Flanking Active TSS	NHEK	skin
6	chr4:100379800-100380400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:100379800-100380600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:100379800-100380600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:100380000-100380400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr4:100380000-100380400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:100380000-100380600	Active TSS	HMEC	breast
12	chr4:100380000-100381000	Enhancers	Placenta	Placenta
13	chr4:100380200-100380600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr4:100380200-100380600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:100380200-100380600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:100380200-100380600	Flanking Active TSS	Liver	Liver
17	chr4:100380200-100380800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:100380200-100380800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:100380200-100380800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr4:100380200-100380800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:100380200-100381000	Enhancers	Fetal Kidney	kidney

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