Variant report

Variant	rs1109088
Chromosome Location	chr3:138154795-138154796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138153677..138156615-chr3:138182530..138184739,2	MCF-7	breast:
2	chr3:138147884..138150331-chr3:138154238..138156616,2	K562	blood:
3	chr3:138150985..138152959-chr3:138153482..138156074,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12631438	0.96[ASN][1000 genomes]
rs12633098	0.91[ASN][1000 genomes]
rs12638938	0.93[ASN][1000 genomes]
rs1546758	0.96[ASN][1000 genomes]
rs1679153	0.91[ASN][1000 genomes]
rs1679170	0.94[ASN][1000 genomes]
rs1679176	0.84[ASN][1000 genomes]
rs1679177	0.84[ASN][1000 genomes]
rs1679179	0.97[ASN][1000 genomes]
rs1679181	0.97[ASN][1000 genomes]
rs1720826	0.84[ASN][1000 genomes]
rs1720829	0.97[ASN][1000 genomes]
rs1720830	0.84[ASN][1000 genomes]
rs1720832	0.83[ASN][1000 genomes]
rs34963112	0.83[ASN][1000 genomes]
rs7609893	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611650	0.93[ASN][1000 genomes]
rs774014	0.93[ASN][1000 genomes]
rs812277	0.93[ASN][1000 genomes]
rs940234	0.97[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:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138152200-138155000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:138152400-138154800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:138152600-138154800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
4	chr3:138152600-138154800	Active TSS	Brain Angular Gyrus	brain
5	chr3:138152800-138154800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:138153000-138154800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:138153000-138154800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:138153000-138155000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
9	chr3:138153000-138155000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
10	chr3:138153000-138155200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:138153200-138154800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:138153200-138154800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:138153200-138154800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:138153200-138155000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr3:138153200-138155000	Active TSS	Psoas Muscle	Psoas
16	chr3:138153400-138154800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:138153400-138154800	Flanking Active TSS	Pancreas	Pancrea
18	chr3:138153400-138154800	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:138153400-138155000	Active TSS	NHDF-Ad	bronchial
20	chr3:138153400-138155200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:138153400-138155200	Active TSS	Brain Anterior Caudate	brain
22	chr3:138153600-138155000	Active TSS	Lung	lung
23	chr3:138153800-138154800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
24	chr3:138154000-138154800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr3:138154000-138154800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:138154000-138154800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:138154200-138154800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr3:138154200-138154800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:138154200-138154800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:138154200-138154800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
31	chr3:138154200-138155000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
32	chr3:138154200-138157000	Weak transcription	HSMMtube	muscle
33	chr3:138154400-138154800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:138154400-138154800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr3:138154400-138154800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr3:138154400-138154800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
37	chr3:138154400-138154800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:138154400-138154800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr3:138154400-138155000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:138154400-138155000	Active TSS	Colon Smooth Muscle	Colon
41	chr3:138154400-138155000	Enhancers	Gastric	stomach
42	chr3:138154400-138155200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:138154400-138155600	Bivalent Enhancer	Fetal Heart	heart
44	chr3:138154400-138159200	Weak transcription	HepG2	liver
45	chr3:138154600-138154800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
46	chr3:138154600-138154800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:138154600-138154800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:138154600-138154800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr3:138154600-138154800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:138154600-138154800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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