Variant report

Variant	rs55864663
Chromosome Location	chr3:100098210-100098211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100097843..100099760-chr3:100112170..100114759,2	MCF-7	breast:
2	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
3	chr3:100098158..100099923-chr3:100101288..100104122,2	K562	blood:

Variant related genes	Relation type
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11918399	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919543	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11919627	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16842142	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772687	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55699261	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56012915	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56956506	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57155242	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57166766	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57332305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57703319	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59304656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59396265	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59491720	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59507591	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59509062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60463428	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60999188	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941434	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941452	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941453	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941454	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941473	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873033	0.83[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 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	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:100071000-100103200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:100071400-100105800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:100077000-100106000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:100077200-100105600	Strong transcription	Duodenum Mucosa	Duodenum
8	chr3:100077600-100105200	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:100078800-100103000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:100078800-100104400	Strong transcription	Fetal Intestine Large	intestine
11	chr3:100079400-100103200	Strong transcription	Osteobl	bone
12	chr3:100079400-100107600	Strong transcription	Dnd41	blood
13	chr3:100079600-100106200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:100079800-100106200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:100080200-100104400	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr3:100080200-100106200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:100080600-100105800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:100081000-100104000	Weak transcription	Aorta	Aorta
19	chr3:100081000-100106000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:100081200-100104000	Strong transcription	HSMM	muscle
21	chr3:100081200-100104800	Strong transcription	Adipose Nuclei	Adipose
22	chr3:100081200-100105200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:100081200-100106000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:100081200-100106200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:100081200-100107000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:100081200-100107000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:100081200-100107800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:100081400-100106200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:100081800-100098400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:100081800-100104200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:100081800-100106200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:100082200-100107200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:100082400-100105800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:100083000-100106000	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:100083400-100105200	Strong transcription	Placenta	Placenta
36	chr3:100084800-100105600	Weak transcription	Fetal Heart	heart
37	chr3:100087000-100103600	Weak transcription	Psoas Muscle	Psoas
38	chr3:100087600-100103000	Weak transcription	Brain Angular Gyrus	brain
39	chr3:100087600-100114600	Weak transcription	Small Intestine	intestine
40	chr3:100088800-100098400	Strong transcription	Hela-S3	cervix
41	chr3:100089000-100104200	Strong transcription	Primary T cells from cord blood	blood
42	chr3:100089000-100104600	Strong transcription	A549	lung
43	chr3:100089000-100104800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:100089000-100105800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr3:100089000-100106000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:100089000-100106000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:100089200-100103000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:100089200-100104400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:100089200-100107200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:100089400-100105400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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