Variant report

Variant	rs12499560
Chromosome Location	chr4:7947022-7947023
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7940292..7942827-chr4:7945120..7947736,2	MCF-7	breast:
2	chr4:7939921..7943801-chr4:7946020..7949690,5	MCF-7	breast:
3	chr4:7946085..7948166-chr4:7952831..7955364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12505812	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2386048	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2386049	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2386050	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2386051	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2386053	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28711584	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2891924	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2891926	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4235266	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4555615	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4696685	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696686	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696687	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696824	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696829	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696830	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696832	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57868040	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58012905	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62290603	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66806187	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv593621	chr4:7943106-7969594	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 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	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
2	chr4:7942000-7950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:7942000-7951000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:7942000-7951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:7942200-7947400	Weak transcription	Fetal Brain Male	brain
6	chr4:7942200-7950600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:7942600-7947800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr4:7942800-7948000	Weak transcription	Fetal Kidney	kidney
9	chr4:7943200-7947400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr4:7943200-7947800	Weak transcription	Ovary	ovary
11	chr4:7943600-7950600	Weak transcription	Fetal Heart	heart
12	chr4:7943800-7947400	Weak transcription	Pancreas	Pancrea
13	chr4:7944200-7947800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:7945000-7947600	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:7945400-7947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:7945400-7957400	Weak transcription	Placenta	Placenta
17	chr4:7946200-7947600	Enhancers	Fetal Intestine Large	intestine
18	chr4:7946200-7948400	Enhancers	Fetal Intestine Small	intestine
19	chr4:7946400-7947400	Enhancers	Rectal Smooth Muscle	rectum
20	chr4:7946400-7948000	Enhancers	Colon Smooth Muscle	Colon
21	chr4:7946400-7948200	Enhancers	Fetal Stomach	stomach
22	chr4:7946600-7947800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:7946600-7947800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:7946600-7948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:7946800-7948200	Enhancers	HepG2	liver
26	chr4:7946800-7950800	Weak transcription	Liver	Liver

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