Variant report

Variant	rs56407223
Chromosome Location	chr4:121842336-121842337
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:121836736..121838271-chr4:121841875..121843483,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2122512	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55841702	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56311699	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839170	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72680460	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72680463	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680471	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680473	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72680500	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72682205	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693258	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121798200-121842400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:121813800-121842400	Weak transcription	NHEK	skin
3	chr4:121814600-121842600	Weak transcription	Right Ventricle	heart
4	chr4:121818000-121842400	Weak transcription	NH-A	brain
5	chr4:121823800-121842400	Weak transcription	HSMM	muscle
6	chr4:121825000-121842600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:121825600-121842400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:121827600-121842400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:121837000-121842800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:121837400-121842600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:121838400-121842400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:121838400-121842400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:121838400-121842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:121838400-121842600	Weak transcription	Gastric	stomach
15	chr4:121838600-121842400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:121838800-121842400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:121839200-121842600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:121839200-121842600	Enhancers	Fetal Intestine Small	intestine
19	chr4:121839400-121842400	Enhancers	Fetal Intestine Large	intestine
20	chr4:121839400-121842600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr4:121839600-121842400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:121839800-121842400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr4:121839800-121842400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr4:121839800-121842400	Enhancers	NHDF-Ad	bronchial
25	chr4:121840000-121842600	Enhancers	Colon Smooth Muscle	Colon
26	chr4:121840000-121842600	Enhancers	Stomach Smooth Muscle	stomach
27	chr4:121840200-121842600	Weak transcription	Esophagus	oesophagus
28	chr4:121840200-121842600	Weak transcription	Left Ventricle	heart
29	chr4:121840200-121842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:121840400-121842400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:121840400-121842600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:121840400-121842600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:121840400-121842600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:121840400-121842600	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:121840400-121842600	Weak transcription	Small Intestine	intestine
36	chr4:121840400-121842600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:121840400-121842800	Weak transcription	Aorta	Aorta
38	chr4:121840600-121842400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:121840600-121842400	Weak transcription	Fetal Heart	heart
40	chr4:121840600-121842400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:121840600-121842400	Weak transcription	Stomach Mucosa	stomach
42	chr4:121840600-121842600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:121840600-121842600	Weak transcription	Brain Substantia Nigra	brain
44	chr4:121840600-121842600	Weak transcription	Fetal Stomach	stomach
45	chr4:121840600-121842600	Weak transcription	Psoas Muscle	Psoas
46	chr4:121840600-121842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:121840800-121842400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:121841000-121842600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:121841000-121842600	Weak transcription	Colonic Mucosa	Colon
50	chr4:121841000-121842600	Weak transcription	Fetal Kidney	kidney

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