Variant report

Variant	rs60049195
Chromosome Location	chr3:42773100-42773101
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	chr3:42770931..42773335-chr3:42773656..42775532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244607	Chromatin interaction
ENSG00000173811	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10461012	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865920	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865921	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865923	0.89[EUR][1000 genomes]
rs11129969	0.98[EUR][1000 genomes]
rs11129970	0.98[EUR][1000 genomes]
rs11709054	0.95[EUR][1000 genomes]
rs11709500	0.96[EUR][1000 genomes]
rs11713172	0.98[EUR][1000 genomes]
rs11915803	0.93[EUR][1000 genomes]
rs17074778	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238314	0.98[EUR][1000 genomes]
rs17238798	0.93[EUR][1000 genomes]
rs2240861	0.95[EUR][1000 genomes]
rs34110933	0.95[EUR][1000 genomes]
rs4682856	0.87[EUR][1000 genomes]
rs55884426	0.97[EUR][1000 genomes]
rs55904344	0.96[EUR][1000 genomes]
rs59478814	0.97[EUR][1000 genomes]
rs59713146	0.98[EUR][1000 genomes]
rs60176972	0.88[EUR][1000 genomes]
rs62246603	0.96[EUR][1000 genomes]
rs62246606	0.95[EUR][1000 genomes]
rs62246635	0.85[EUR][1000 genomes]
rs62250113	0.95[EUR][1000 genomes]
rs62250114	0.96[EUR][1000 genomes]
rs6442057	0.92[EUR][1000 genomes]
rs9836162	0.95[EUR][1000 genomes]
rs9837412	0.88[EUR][1000 genomes]
rs9838388	0.87[EUR][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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42760400-42773600	Enhancers	Brain Substantia Nigra	brain
2	chr3:42763600-42773600	Enhancers	Brain Anterior Caudate	brain
3	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
4	chr3:42767800-42774400	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:42769000-42773600	Enhancers	Brain Hippocampus Middle	brain
7	chr3:42769000-42774200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:42769000-42774800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:42769000-42775000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:42769800-42773200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:42769800-42774200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:42769800-42787600	Weak transcription	Gastric	stomach
14	chr3:42770200-42774200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:42770600-42775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:42770800-42773400	Enhancers	Fetal Heart	heart
17	chr3:42771000-42774000	Enhancers	Right Ventricle	heart
18	chr3:42771000-42774200	Enhancers	Right Atrium	heart
19	chr3:42771200-42773400	Enhancers	HepG2	liver
20	chr3:42771200-42775800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:42771600-42773200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:42772200-42773800	Weak transcription	Psoas Muscle	Psoas
23	chr3:42772600-42773600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
25	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:42772800-42773200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:42773000-42774600	Enhancers	Pancreas	Pancrea
28	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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