Variant report

Variant	rs55664415
Chromosome Location	chr3:52124885-52124886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52111491..52114530-chr3:52124287..52129242,4	K562	blood:
2	chr3:52095912..52098452-chr3:52124291..52126247,2	K562	blood:
3	chr3:52123230..52125073-chr3:52183887..52186377,2	MCF-7	breast:
4	chr3:52124027..52125653-chr3:52126066..52128090,2	MCF-7	breast:
5	chr3:52105087..52107188-chr3:52123209..52125122,2	K562	blood:
6	chr3:52115096..52116701-chr3:52123707..52125546,2	K562	blood:

Variant related genes	Relation type
ENSG00000256097	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs123681	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12386365	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13314125	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13319566	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164638	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164639	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051957	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17051977	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs171294	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs183029	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2304505	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28452586	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28659792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352146	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352147	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352148	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352149	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352150	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352151	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs352153	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55834589	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56281986	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56322622	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57335685	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57466127	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59890038	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6781635	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72964042	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72964044	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638246	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs808787	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs876782	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs893056	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9809254	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9809977	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9811707	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9815010	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9816434	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817653	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830293	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841469	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843299	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843852	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846049	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847073	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847092	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9857878	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9860982	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868101	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9882775	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
6	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52105800-52142400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:52109600-52129800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:52110000-52125000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:52110000-52126000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:52110000-52126000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:52110000-52127000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:52110000-52127200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:52110000-52127400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:52110200-52125400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:52110600-52179400	Weak transcription	Brain Germinal Matrix	brain
11	chr3:52111200-52127000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:52115800-52133000	Weak transcription	Gastric	stomach
13	chr3:52119200-52126800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:52119200-52127200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:52119200-52128400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:52119200-52128600	Enhancers	Fetal Muscle Trunk	muscle
17	chr3:52119600-52129000	Enhancers	Fetal Muscle Leg	muscle
18	chr3:52120000-52125400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:52120600-52125000	Enhancers	HepG2	liver
20	chr3:52120600-52125400	Enhancers	HUVEC	blood vessel
21	chr3:52120600-52126200	Enhancers	Adipose Nuclei	Adipose
22	chr3:52120600-52126600	Enhancers	Left Ventricle	heart
23	chr3:52120600-52128800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:52120600-52128800	Enhancers	Placenta	Placenta
25	chr3:52120600-52129200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:52120800-52125400	Enhancers	Fetal Intestine Large	intestine
27	chr3:52120800-52125800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:52120800-52125800	Enhancers	K562	blood
29	chr3:52120800-52127400	Enhancers	Right Atrium	heart
30	chr3:52121000-52126200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:52121000-52128400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:52121000-52128400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:52121200-52128400	Enhancers	NHDF-Ad	bronchial
34	chr3:52121400-52129000	Weak transcription	Primary T cells from cord blood	blood
35	chr3:52121600-52126200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:52121800-52126200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:52122000-52125200	Enhancers	Stomach Smooth Muscle	stomach
38	chr3:52122000-52126200	Enhancers	Placenta Amnion	Placenta Amnion
39	chr3:52122000-52140000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52122200-52125600	Genic enhancers	Fetal Intestine Small	intestine
41	chr3:52122200-52126000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52122200-52126200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52122200-52126400	Enhancers	Fetal Lung	lung
44	chr3:52122200-52128200	Enhancers	Brain Hippocampus Middle	brain
45	chr3:52122400-52126000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:52122400-52126600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:52122400-52126600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:52122400-52130400	Enhancers	Fetal Heart	heart
49	chr3:52122600-52125200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:52122600-52125800	Weak transcription	Esophagus	oesophagus

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