Variant report

Variant	rs1720832
Chromosome Location	chr3:138161109-138161110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138152454..138155577-chr3:138156985..138161293,10	MCF-7	breast:
2	chr3:138159991..138162907-chr3:138171980..138174435,2	MCF-7	breast:
3	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:27)

rs_ID	r²[population]
rs1109088	0.83[ASN][1000 genomes]
rs12631438	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs12633098	0.88[ASN][1000 genomes]
rs12638938	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1403776	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1403777	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1546758	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs1679153	0.88[CHB][hapmap]
rs1679170	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1679176	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679177	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679179	0.86[ASN][1000 genomes]
rs1679181	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs171693	1.00[EUR][1000 genomes]
rs1720826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1720829	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs1720830	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34963112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775027	0.90[EUR][1000 genomes]
rs7609893	0.83[ASN][1000 genomes]
rs7611650	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs774013	0.82[ASN][1000 genomes]
rs774014	0.85[ASN][1000 genomes]
rs774374	1.00[EUR][1000 genomes]
rs809573	1.00[EUR][1000 genomes]
rs812277	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs940234	0.86[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:50 , 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	chr3:138155600-138161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:138156000-138175800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:138156600-138170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:138157000-138163400	Enhancers	HSMMtube	muscle
7	chr3:138157400-138163400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:138157600-138161400	Enhancers	HSMM	muscle
9	chr3:138157600-138162600	Enhancers	NHDF-Ad	bronchial
10	chr3:138157800-138161800	Enhancers	Osteobl	bone
11	chr3:138158000-138163400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:138158200-138161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:138158200-138161600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:138158200-138161800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr3:138158400-138161400	Enhancers	Fetal Muscle Trunk	muscle
16	chr3:138158800-138162000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:138159000-138161400	Enhancers	NH-A	brain
18	chr3:138159000-138162400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:138159000-138162400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:138159000-138164600	Enhancers	Fetal Muscle Leg	muscle
21	chr3:138159200-138162200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:138159800-138161400	Weak transcription	HepG2	liver
23	chr3:138160000-138161400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:138160200-138161800	Weak transcription	Fetal Lung	lung
25	chr3:138160400-138161400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:138160400-138161400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:138160400-138161400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:138160400-138161400	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:138160400-138161400	Weak transcription	Fetal Stomach	stomach
30	chr3:138160400-138161400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr3:138160400-138161800	Weak transcription	Fetal Heart	heart
32	chr3:138160400-138169400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:138160600-138161400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:138160600-138161400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:138160600-138161400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:138160600-138161800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:138160600-138162000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:138160600-138162000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:138160600-138162200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:138160600-138162200	Weak transcription	Lung	lung
41	chr3:138160600-138170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:138160800-138161200	Enhancers	Hela-S3	cervix
43	chr3:138160800-138161400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:138160800-138161400	Flanking Active TSS	A549	lung
45	chr3:138160800-138161400	Enhancers	NHEK	skin
46	chr3:138160800-138161800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:138160800-138162400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:138161000-138161200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:138161000-138161200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:138161000-138161600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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