Variant report

Variant	rs1720829
Chromosome Location	chr3:138158992-138158993
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	chr3:138152454..138155577-chr3:138156985..138161293,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10513053	1.00[CEU][hapmap]
rs1109088	0.97[ASN][1000 genomes]
rs11916525	0.80[JPT][hapmap]
rs12630060	0.80[JPT][hapmap]
rs12631438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632794	0.80[JPT][hapmap]
rs12633098	0.93[ASN][1000 genomes]
rs12635904	0.80[JPT][hapmap]
rs12637679	0.81[JPT][hapmap]
rs12638938	0.96[ASN][1000 genomes]
rs13059817	0.81[JPT][hapmap]
rs13062423	0.81[JPT][hapmap]
rs13084780	0.80[JPT][hapmap]
rs13098554	0.81[JPT][hapmap]
rs1546758	0.82[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1679153	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1679170	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1679176	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs1679177	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs1679179	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1720826	0.87[ASN][1000 genomes]
rs1720830	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs1720832	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs34963112	0.86[ASN][1000 genomes]
rs6768963	0.81[JPT][hapmap]
rs7609893	0.97[ASN][1000 genomes]
rs7611650	0.96[ASN][1000 genomes]
rs774014	0.96[ASN][1000 genomes]
rs811794	0.91[JPT][hapmap]
rs812277	0.88[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.96[ASN][1000 genomes]
rs9049	0.80[JPT][hapmap]
rs940234	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138154400-138159200	Weak transcription	HepG2	liver
2	chr3:138154600-138159200	Weak transcription	Right Ventricle	heart
3	chr3:138154800-138160000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:138155000-138159000	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr3:138155000-138182800	Weak transcription	Gastric	stomach
6	chr3:138155200-138169200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:138155600-138161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:138156000-138175800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:138156600-138170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:138156800-138159600	Weak transcription	Lung	lung
11	chr3:138157000-138163400	Enhancers	HSMMtube	muscle
12	chr3:138157400-138159800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:138157400-138163400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:138157600-138160600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:138157600-138161400	Enhancers	HSMM	muscle
16	chr3:138157600-138162600	Enhancers	NHDF-Ad	bronchial
17	chr3:138157800-138160000	Bivalent Enhancer	Fetal Stomach	stomach
18	chr3:138157800-138161800	Enhancers	Osteobl	bone
19	chr3:138158000-138160400	Enhancers	Colon Smooth Muscle	Colon
20	chr3:138158000-138163400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:138158200-138160600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:138158200-138161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:138158200-138161600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:138158200-138161800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr3:138158400-138160400	Enhancers	Fetal Heart	heart
26	chr3:138158400-138160800	Enhancers	Stomach Smooth Muscle	stomach
27	chr3:138158400-138161400	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:138158600-138159400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:138158600-138159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:138158600-138160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:138158800-138159000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:138158800-138160000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:138158800-138160400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:138158800-138160400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:138158800-138160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:138158800-138162000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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