Variant report

Variant	rs12644609
Chromosome Location	chr4:7974048-7974049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7968293..7969808-chr4:7972289..7974865,2	MCF-7	breast:
2	chr4:7972595..7975049-chr4:7979721..7982181,5	MCF-7	breast:
3	chr4:7938506..7945813-chr4:7968503..7977501,21	MCF-7	breast:
4	chr4:7943385..7945490-chr4:7973996..7976275,2	MCF-7	breast:
5	chr4:7940228..7942732-chr4:7972694..7975678,3	MCF-7	breast:
6	chr4:7972328..7974698-chr4:7988025..7989740,2	MCF-7	breast:
7	chr4:7973238..7976056-chr4:7980066..7981632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1317282	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1878323	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2386052	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447897	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7654924	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7677869	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs870714	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv878579	chr4:7969594-8011696	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases
9	esv18370	chr4:7971253-7974932	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv593622	chr4:7971872-7974747	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7963400-7975400	Weak transcription	Aorta	Aorta
2	chr4:7967000-7987600	Weak transcription	Psoas Muscle	Psoas
3	chr4:7969000-7975600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
4	chr4:7969200-7974400	Enhancers	Fetal Muscle Leg	muscle
5	chr4:7969200-7975600	Enhancers	Fetal Thymus	thymus
6	chr4:7969200-7975800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:7969400-7974800	Enhancers	Lung	lung
8	chr4:7969400-7975800	Enhancers	Stomach Smooth Muscle	stomach
9	chr4:7969400-7976000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:7969600-7975800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr4:7970400-7980200	Weak transcription	HSMM	muscle
12	chr4:7970800-7975800	Enhancers	NH-A	brain
13	chr4:7971000-7974600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:7971000-7976000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:7971000-7976000	Enhancers	HMEC	breast
16	chr4:7971200-7976000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:7971400-7974600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:7971400-7974600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr4:7971400-7974600	Flanking Active TSS	HepG2	liver
20	chr4:7971400-7975000	Enhancers	Pancreas	Pancrea
21	chr4:7971600-7974800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:7971600-7975800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:7971800-7974200	Weak transcription	Brain Substantia Nigra	brain
24	chr4:7971800-7974400	Flanking Active TSS	Colonic Mucosa	Colon
25	chr4:7971800-7974800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:7972000-7974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:7972000-7974600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:7972000-7975200	Weak transcription	HSMMtube	muscle
29	chr4:7972200-7975400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:7972200-7976200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:7972200-7979600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr4:7972200-7980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:7972400-7974200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:7972400-7974600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr4:7972400-7975200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:7972400-7975400	Weak transcription	Brain Anterior Caudate	brain
37	chr4:7972400-7975600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:7972400-7975600	Enhancers	Esophagus	oesophagus
39	chr4:7972400-7975800	Weak transcription	Colon Smooth Muscle	Colon
40	chr4:7972400-7976000	Enhancers	NHEK	skin
41	chr4:7972400-7978400	Weak transcription	Fetal Kidney	kidney
42	chr4:7972400-7980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr4:7972600-7974400	Weak transcription	Brain Hippocampus Middle	brain
44	chr4:7972600-7975400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:7972600-7975400	Weak transcription	Left Ventricle	heart
46	chr4:7972600-7976000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:7972600-7976000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:7972800-7974200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:7972800-7974400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:7972800-7975400	Weak transcription	Right Atrium	heart

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