Variant report

Variant	rs3769209
Chromosome Location	chr2:173943038-173943039
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173941095..173943931-chr2:174073550..174075773,3	MCF-7	breast:
2	chr2:173942302..173944887-chr2:173980344..173983035,2	K562	blood:
3	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1345008	1.00[CHB][hapmap]
rs1439976	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17302439	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17375006	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17761097	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769186	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769198	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769202	1.00[ASN][1000 genomes]
rs3769221	1.00[CEU][hapmap]
rs3820834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41268711	0.86[AMR][1000 genomes]
rs7585076	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173940000-173943400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr2:173940200-173943200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr2:173940200-173943400	Active TSS	Stomach Smooth Muscle	stomach
4	chr2:173940400-173943200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:173940400-173943200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:173940400-173943200	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr2:173940400-173943600	Active TSS	Right Ventricle	heart
8	chr2:173941200-173943200	Active TSS	Right Atrium	heart
9	chr2:173941600-173943600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:173941600-173947200	Weak transcription	Gastric	stomach
11	chr2:173941600-173955200	Weak transcription	Lung	lung
12	chr2:173941600-173955200	Weak transcription	Pancreas	Pancrea
13	chr2:173941600-173969600	Weak transcription	Spleen	Spleen
14	chr2:173941800-173943200	Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr2:173941800-173955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:173941800-173955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:173942000-173943800	Weak transcription	Left Ventricle	heart
18	chr2:173942000-173944400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:173942000-173945000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:173942000-173946600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:173942000-173951400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:173942000-173953000	Weak transcription	Stomach Mucosa	stomach
23	chr2:173942000-173955200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:173942000-173955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:173942000-173956000	Weak transcription	Fetal Thymus	thymus
26	chr2:173942200-173943200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:173942200-173943200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:173942200-173943400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:173942200-173943400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:173942200-173943400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:173942200-173943400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:173942200-173943400	Enhancers	HepG2	liver
33	chr2:173942200-173943800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:173942200-173943800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr2:173942200-173946200	Weak transcription	Primary T cells from cord blood	blood
36	chr2:173942400-173943200	Flanking Active TSS	NHEK	skin
37	chr2:173942400-173943400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:173942400-173943400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:173942400-173943400	Flanking Active TSS	GM12878-XiMat	blood
40	chr2:173942600-173943200	Flanking Active TSS	Fetal Heart	heart
41	chr2:173942600-173943200	Flanking Active TSS	Hela-S3	cervix
42	chr2:173942600-173943400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:173942600-173943600	Flanking Active TSS	A549	lung
44	chr2:173942600-173944000	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr2:173942600-173944200	Enhancers	Fetal Stomach	stomach
46	chr2:173942600-173956400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:173942800-173943200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:173942800-173943200	Active TSS	Aorta	Aorta
49	chr2:173942800-173943200	Enhancers	Fetal Brain Female	brain
50	chr2:173942800-173943400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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