Variant report

Variant	rs59217491
Chromosome Location	chr3:138162045-138162046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138159991..138162907-chr3:138171980..138174435,2	MCF-7	breast:
2	chr3:138152375..138158526-chr3:138160154..138163422,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10513053	0.95[ASN][1000 genomes]
rs11923795	0.95[ASN][1000 genomes]
rs12695685	0.84[ASN][1000 genomes]
rs13074317	0.84[ASN][1000 genomes]
rs13079209	0.84[ASN][1000 genomes]
rs13080413	0.84[ASN][1000 genomes]
rs13083299	0.84[ASN][1000 genomes]
rs13096934	0.84[ASN][1000 genomes]
rs2279241	0.84[ASN][1000 genomes]
rs2291127	0.84[ASN][1000 genomes]
rs2293251	0.84[ASN][1000 genomes]
rs2306374	0.84[ASN][1000 genomes]
rs2347252	0.84[ASN][1000 genomes]
rs34078858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34382779	0.95[ASN][1000 genomes]
rs34568901	0.84[ASN][1000 genomes]
rs3732837	0.84[ASN][1000 genomes]
rs3773750	0.84[ASN][1000 genomes]
rs57521136	0.95[ASN][1000 genomes]
rs58059555	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71312578	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9818870	0.84[ASN][1000 genomes]
rs9828345	0.95[ASN][1000 genomes]
rs9843291	0.95[ASN][1000 genomes]
rs9848655	0.84[ASN][1000 genomes]
rs9851766	0.84[ASN][1000 genomes]
rs9864898	0.84[ASN][1000 genomes]
rs9872754	0.84[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	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers 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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138155000-138182800	Weak transcription	Gastric	stomach
2	chr3:138155200-138169200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:138156000-138175800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:138156600-138170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:138157000-138163400	Enhancers	HSMMtube	muscle
6	chr3:138157400-138163400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:138157600-138162600	Enhancers	NHDF-Ad	bronchial
8	chr3:138158000-138163400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:138159000-138162400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:138159000-138162400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:138159000-138164600	Enhancers	Fetal Muscle Leg	muscle
12	chr3:138159200-138162200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:138160400-138169400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:138160600-138162200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:138160600-138162200	Weak transcription	Lung	lung
16	chr3:138160600-138170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:138160800-138162400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:138161200-138162200	Enhancers	K562	blood
19	chr3:138161400-138162200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:138161400-138162400	Enhancers	HepG2	liver
21	chr3:138161400-138162400	Weak transcription	HSMM	muscle
22	chr3:138161400-138162600	Enhancers	Rectal Smooth Muscle	rectum
23	chr3:138161400-138162800	Enhancers	Colon Smooth Muscle	Colon
24	chr3:138161400-138162800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:138161400-138163800	Enhancers	Fetal Stomach	stomach
26	chr3:138161600-138162800	Enhancers	Fetal Intestine Large	intestine
27	chr3:138161600-138162800	Enhancers	Fetal Intestine Small	intestine
28	chr3:138161600-138163000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:138161600-138169600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:138161600-138170000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:138161800-138162400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:138161800-138163000	Enhancers	Fetal Brain Male	brain
34	chr3:138161800-138163200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:138161800-138163600	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:138161800-138164400	Enhancers	Fetal Heart	heart
37	chr3:138161800-138164600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:138162000-138162400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:138162000-138162400	Weak transcription	Fetal Lung	lung
40	chr3:138162000-138167600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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