Variant report

Variant	rs61825239
Chromosome Location	chr1:184547419-184547420
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184537183..184539012-chr1:184545645..184548048,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116667	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10489729	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911610	0.87[ASN][1000 genomes]
rs12075202	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12089761	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12097916	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239499	0.82[ASN][1000 genomes]
rs16823311	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823313	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16823318	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1969683	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56350837	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57780220	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61643431	0.93[ASN][1000 genomes]
rs61825204	0.80[AFR][1000 genomes]
rs6669940	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693408	0.81[ASN][1000 genomes]
rs6695173	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72737723	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530615	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7532351	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184536000-184559000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:184536000-184559000	Weak transcription	NHEK	skin
3	chr1:184536200-184549200	Weak transcription	NHDF-Ad	bronchial
4	chr1:184536800-184559200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:184537200-184559000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:184538000-184559400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:184538400-184558000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:184538400-184558000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:184538400-184559000	Weak transcription	Right Atrium	heart
10	chr1:184538600-184549000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:184538800-184548600	Weak transcription	Fetal Intestine Small	intestine
12	chr1:184544200-184551200	Weak transcription	Small Intestine	intestine
13	chr1:184544400-184552800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:184544600-184552400	Weak transcription	Fetal Lung	lung
15	chr1:184545600-184547600	Enhancers	Adipose Nuclei	Adipose
16	chr1:184546200-184551600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:184546200-184563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:184546200-184566600	Weak transcription	Left Ventricle	heart
19	chr1:184546600-184547800	Weak transcription	Fetal Stomach	stomach
20	chr1:184546800-184556600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:184547000-184547600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:184547000-184549000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:184547400-184547600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:184547400-184547800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:184547400-184547800	Enhancers	Colon Smooth Muscle	Colon
26	chr1:184547400-184549000	Weak transcription	Psoas Muscle	Psoas

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