Variant report

Variant	rs7429840
Chromosome Location	chr3:133965193-133965194
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:133965027..133966647-chr3:134091891..134094278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10935104	0.85[ASN][1000 genomes]
rs12635994	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13068409	0.84[ASN][1000 genomes]
rs13099506	0.88[ASN][1000 genomes]
rs28514329	0.92[ASN][1000 genomes]
rs35111284	0.93[ASN][1000 genomes]
rs35775034	0.84[ASN][1000 genomes]
rs4077158	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077643	0.93[ASN][1000 genomes]
rs4280635	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4404422	0.93[ASN][1000 genomes]
rs6439464	0.86[ASN][1000 genomes]
rs6439469	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs67022177	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6783086	0.93[ASN][1000 genomes]
rs6783294	0.91[ASN][1000 genomes]
rs6786384	0.82[ASN][1000 genomes]
rs6795164	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6796404	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804370	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73215351	0.82[ASN][1000 genomes]
rs7623609	0.88[ASN][1000 genomes]
rs7639683	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7641162	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809556	0.93[ASN][1000 genomes]
rs9822076	0.86[ASN][1000 genomes]
rs9822469	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9822749	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9829505	0.91[ASN][1000 genomes]
rs9839609	0.93[ASN][1000 genomes]
rs9846664	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9858000	0.88[ASN][1000 genomes]
rs9859680	0.92[ASN][1000 genomes]
rs9865808	0.93[ASN][1000 genomes]
rs9880098	0.93[ASN][1000 genomes]
rs9881896	0.91[ASN][1000 genomes]
rs9882168	0.88[ASN][1000 genomes]
rs9882590	0.84[ASN][1000 genomes]
rs9882927	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv1794616	chr3:133949713-133973731	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	esv1798974	chr3:133949713-133973731	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv1802675	chr3:133949713-133973731	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv1815799	chr3:133949713-133973731	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv1819695	chr3:133949713-133973731	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv1822126	chr3:133949713-133973731	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	esv1839030	chr3:133949713-133973731	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	esv1799165	chr3:133959746-133973731	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	esv1803106	chr3:133959746-133973731	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133930200-133968000	Weak transcription	Fetal Kidney	kidney
2	chr3:133941400-133967400	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:133951200-133966800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:133952200-133965400	Weak transcription	Dnd41	blood
5	chr3:133953200-133967800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:133953400-133966800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:133957600-133967000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:133957600-133968000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:133957600-133968000	Weak transcription	Fetal Stomach	stomach
10	chr3:133958400-133966800	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:133958800-133966800	Weak transcription	Gastric	stomach
12	chr3:133958800-133967200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:133958800-133967800	Weak transcription	Stomach Mucosa	stomach
14	chr3:133958800-133968200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:133959000-133967600	Weak transcription	GM12878-XiMat	blood
16	chr3:133959000-133968200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:133959000-133968800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:133959200-133967800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:133959600-133967800	Enhancers	HepG2	liver
20	chr3:133960000-133966800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:133960600-133965200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:133961600-133965800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:133961800-133966000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:133962000-133966800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:133962000-133967000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:133962000-133967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:133962000-133968200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:133962200-133965400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:133962200-133967000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:133962200-133967000	Weak transcription	Fetal Brain Female	brain
31	chr3:133962200-133967600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:133962200-133967600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:133962400-133965600	Weak transcription	Liver	Liver
34	chr3:133962400-133965800	Weak transcription	A549	lung
35	chr3:133962400-133966800	Weak transcription	Right Ventricle	heart
36	chr3:133962400-133966800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:133962400-133967000	Weak transcription	Esophagus	oesophagus
38	chr3:133962400-133967600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:133962400-133967600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:133962400-133968000	Weak transcription	HSMMtube	muscle
41	chr3:133962400-133968200	Weak transcription	Aorta	Aorta
42	chr3:133962400-133968200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:133962600-133966000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:133962600-133967000	Weak transcription	Primary T cells from cord blood	blood
45	chr3:133962600-133967200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:133962600-133967600	Weak transcription	HSMM	muscle
47	chr3:133962600-133967600	Weak transcription	NH-A	brain
48	chr3:133962600-133967600	Weak transcription	Osteobl	bone
49	chr3:133962600-133968000	Weak transcription	Fetal Intestine Small	intestine
50	chr3:133962800-133967200	Weak transcription	Muscle Satellite Cultured Cells	--

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