Variant report

Variant	rs74046554
Chromosome Location	chr13:40135273-40135274
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	chr13:40126439..40128826-chr13:40132731..40135327,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17060288	0.80[ASN][1000 genomes]
rs56103901	0.96[ASN][1000 genomes]
rs56213801	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57628663	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61432896	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61954148	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61956463	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61956464	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61956467	0.96[ASN][1000 genomes]
rs7317222	0.98[ASN][1000 genomes]
rs7334762	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74044105	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs74046534	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74046537	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74046538	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74046541	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74046546	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74046552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74046553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74046555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74046556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983392	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7985820	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7985865	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7987557	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9532392	0.98[ASN][1000 genomes]
rs978136	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:40114400-40136000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr13:40121400-40136200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr13:40126400-40137200	Weak transcription	NHLF	lung
5	chr13:40127000-40136200	Weak transcription	NHDF-Ad	bronchial
6	chr13:40128800-40137600	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:40129200-40135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:40129200-40135800	Weak transcription	HMEC	breast
11	chr13:40129400-40136800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:40130000-40139600	Weak transcription	Fetal Stomach	stomach
13	chr13:40131000-40138600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:40131000-40138600	Weak transcription	Adipose Nuclei	Adipose
15	chr13:40131200-40137600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:40131600-40135400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:40131600-40137400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr13:40132000-40136200	Weak transcription	HSMM	muscle
19	chr13:40132200-40136200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:40132200-40145600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr13:40132400-40135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr13:40132400-40137600	Weak transcription	Fetal Lung	lung
23	chr13:40133200-40135400	Enhancers	HSMMtube	muscle
24	chr13:40133400-40136800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:40133600-40137400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:40133600-40137600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr13:40133800-40137000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:40133800-40137400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr13:40133800-40137600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr13:40133800-40138000	Weak transcription	Aorta	Aorta
31	chr13:40133800-40138200	Weak transcription	Brain Substantia Nigra	brain
32	chr13:40134000-40139400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:40134200-40137000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:40134200-40137200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr13:40134200-40139800	Weak transcription	Fetal Muscle Leg	muscle
36	chr13:40134400-40137000	Weak transcription	Fetal Heart	heart
37	chr13:40134400-40137400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr13:40134400-40137600	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:40134600-40136800	Weak transcription	Osteobl	bone
40	chr13:40134800-40135400	Enhancers	Left Ventricle	heart
41	chr13:40134800-40135600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:40135000-40135400	Enhancers	Right Atrium	heart
43	chr13:40135000-40136000	Enhancers	Ovary	ovary
44	chr13:40135200-40135400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr13:40135200-40135600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:40135200-40135800	Enhancers	Lung	lung
47	chr13:40135200-40136000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:40135200-40136400	Enhancers	Right Ventricle	heart
49	chr13:40135200-40137400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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