Variant report

Variant	rs7619643
Chromosome Location	chr3:52788119-52788120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52787616..52789879-chr3:52803393..52805587,2	MCF-7	breast:
2	chr3:52788031..52789791-chr3:52792352..52793907,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10510759	0.85[AMR][1000 genomes]
rs1987234	0.85[AMR][1000 genomes]
rs35920544	0.85[AMR][1000 genomes]
rs56156188	0.85[AMR][1000 genomes]
rs56259931	0.85[AMR][1000 genomes]
rs57008939	0.85[AMR][1000 genomes]
rs57246324	0.85[AMR][1000 genomes]
rs57319306	0.85[AMR][1000 genomes]
rs57560655	0.85[AMR][1000 genomes]
rs58100002	0.85[AMR][1000 genomes]
rs58725214	0.85[AMR][1000 genomes]
rs60415551	0.85[AMR][1000 genomes]
rs60823713	0.85[AMR][1000 genomes]
rs60916588	0.85[AMR][1000 genomes]
rs61220667	1.00[AMR][1000 genomes]
rs6445536	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6769720	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947580	0.85[AMR][1000 genomes]
rs72947589	0.85[AMR][1000 genomes]
rs72950430	0.85[AMR][1000 genomes]
rs72950432	0.85[AMR][1000 genomes]
rs72960240	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72960281	1.00[AMR][1000 genomes]
rs7647992	0.85[AMR][1000 genomes]
rs7648016	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:52763800-52788400	Strong transcription	Fetal Brain Female	brain
4	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
10	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
11	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:52765600-52788800	Strong transcription	Brain Anterior Caudate	brain
13	chr3:52765600-52789000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:52765600-52789400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr3:52766200-52789600	Strong transcription	Placenta	Placenta
16	chr3:52766400-52789400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
18	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
21	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:52768000-52789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:52768400-52797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:52768800-52803000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:52770200-52789000	Strong transcription	Fetal Stomach	stomach
27	chr3:52770200-52797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:52770800-52789400	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:52771000-52788800	Strong transcription	Lung	lung
30	chr3:52771200-52788800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:52771200-52789400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:52771200-52800800	Strong transcription	Fetal Lung	lung
33	chr3:52771400-52788200	Strong transcription	Left Ventricle	heart
34	chr3:52772000-52788600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:52772600-52794800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:52774000-52803400	Weak transcription	K562	blood
37	chr3:52774400-52789200	Strong transcription	Fetal Intestine Small	intestine
38	chr3:52775200-52788600	Strong transcription	Brain Hippocampus Middle	brain
39	chr3:52775200-52788800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:52775200-52800600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:52775200-52802600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:52775400-52788400	Strong transcription	Brain Angular Gyrus	brain
43	chr3:52775400-52789000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr3:52775600-52789400	Strong transcription	Primary T cells from cord blood	blood
45	chr3:52775800-52789400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:52775800-52802800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:52775800-52802800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:52776000-52788400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:52776000-52788800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:52776000-52794200	Strong transcription	Brain Inferior Temporal Lobe	brain

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