Variant report

Variant	rs4855872
Chromosome Location	chr3:49460910-49460911
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49456096-49460980	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49460325..49461920-chr3:49506460..49509220,2	MCF-7	breast:
2	chr3:49375139..49377482-chr3:49460180..49462859,2	MCF-7	breast:
3	chr3:49460720..49464051-chr3:49464777..49467713,3	MCF-7	breast:
4	chr3:49457686..49462880-chr3:49464384..49468098,7	MCF-7	breast:
5	chr3:49377853..49379731-chr3:49460064..49462187,2	K562	blood:
6	chr3:49448910..49451821-chr3:49459047..49464749,5	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCTA-1	chr3:49460379-49460958	ENSG00000235261.1

No data

Variant related genes	Relation type
AMT	TF binding region
ENSG00000173402	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000145029	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11717485	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.82[AFR][1000 genomes]
rs1996874	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	1.00[EUR][1000 genomes]
rs2311794	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	1.00[EUR][1000 genomes]
rs2329024	1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	1.00[EUR][1000 genomes]
rs3870340	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[EUR][1000 genomes]
rs4241409	0.90[AFR][1000 genomes]
rs4452334	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[EUR][1000 genomes]
rs4855856	1.00[EUR][1000 genomes]
rs4855857	1.00[EUR][1000 genomes]
rs4855870	0.90[AFR][1000 genomes]
rs4855874	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[EUR][1000 genomes]
rs4855878	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[EUR][1000 genomes]
rs55808753	0.90[AFR][1000 genomes]
rs55990645	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	1.00[EUR][1000 genomes]
rs56897974	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60011446	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.87[AFR][1000 genomes]
rs6446270	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	1.00[EUR][1000 genomes]
rs6446279	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.82[AFR][1000 genomes]
rs6446281	1.00[EUR][1000 genomes]
rs6446282	1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	0.83[AFR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	1.00[EUR][1000 genomes]
rs73831435	1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	1.00[EUR][1000 genomes]
rs73831442	0.82[AFR][1000 genomes]
rs7646393	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.90[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[EUR][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
2	chr3:49455400-49461800	Weak transcription	Aorta	Aorta
3	chr3:49455600-49461600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:49455600-49461800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:49455800-49463800	Strong transcription	Dnd41	blood
7	chr3:49457000-49461600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:49457400-49461200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:49457400-49466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:49457600-49465400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:49457800-49461600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:49458200-49461800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:49459200-49462200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr3:49459200-49466200	Weak transcription	HUVEC	blood vessel
15	chr3:49459400-49461800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:49459400-49465800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:49459600-49461600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:49459600-49461800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:49459600-49465200	Weak transcription	Hela-S3	cervix
20	chr3:49459600-49465600	Weak transcription	NHDF-Ad	bronchial
21	chr3:49459600-49466200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:49459600-49466200	Weak transcription	HMEC	breast
23	chr3:49459800-49461000	Enhancers	Placenta	Placenta
24	chr3:49459800-49461400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:49459800-49461800	Weak transcription	GM12878-XiMat	blood
26	chr3:49459800-49465600	Weak transcription	NHEK	skin
27	chr3:49460000-49461000	Genic enhancers	Fetal Muscle Leg	muscle
28	chr3:49460000-49461400	Weak transcription	Fetal Brain Female	brain
29	chr3:49460200-49461000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:49460200-49461400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:49460200-49461600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:49460200-49461800	Weak transcription	Primary B cells from cord blood	blood
33	chr3:49460200-49461800	Weak transcription	Ovary	ovary
34	chr3:49460200-49461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:49460200-49462200	Genic enhancers	Primary T cells from cord blood	blood
36	chr3:49460200-49463600	Strong transcription	Brain Germinal Matrix	brain
37	chr3:49460200-49463800	Strong transcription	Lung	lung
38	chr3:49460200-49466000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr3:49460400-49461000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:49460400-49461000	Enhancers	Liver	Liver
41	chr3:49460400-49461000	Genic enhancers	Fetal Intestine Small	intestine
42	chr3:49460400-49461200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:49460400-49461200	Enhancers	Pancreas	Pancrea
44	chr3:49460400-49461600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:49460400-49461600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:49460400-49461800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:49460400-49461800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:49460400-49461800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:49460400-49461800	Weak transcription	Gastric	stomach
50	chr3:49460400-49462000	Weak transcription	Primary monocytes fromperipheralblood	blood

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