Variant report

Variant	rs62619200
Chromosome Location	chr3:53924996-53924997
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
2	chr3:53924684..53925501-chr7:135346877..135347648,2	NB4	blood:
3	chr3:53909521..53911477-chr3:53924349..53927028,2	MCF-7	breast:
4	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
5	chr3:53921644..53923214-chr3:53923445..53925751,2	MCF-7	breast:
6	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTR8-2	chr3:53924953-53925087	NONHSAT090009

No data

Variant related genes	Relation type
ENSG00000113812	Chromatin interaction
ENSG00000243317	Chromatin interaction
ENSG00000222888	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13071560	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13073855	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13088816	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13096326	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2232338	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2232341	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34310576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34431816	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34443284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34549821	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34938855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35222185	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36102758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66535155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66583280	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66720724	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66818866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67340660	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71617207	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53919600-53925200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:53922400-53925000	Enhancers	Small Intestine	intestine
3	chr3:53923400-53925000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr3:53923400-53926400	Active TSS	Right Ventricle	heart
5	chr3:53923600-53926600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr3:53924000-53925000	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:53924000-53925000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:53924000-53925000	Flanking Active TSS	NHEK	skin
9	chr3:53924000-53925200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:53924000-53925200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:53924000-53925200	Flanking Active TSS	Liver	Liver
12	chr3:53924000-53925200	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr3:53924000-53925200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr3:53924000-53925200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr3:53924000-53925200	Enhancers	Spleen	Spleen
16	chr3:53924000-53925200	Flanking Active TSS	Hela-S3	cervix
17	chr3:53924000-53925400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:53924000-53925400	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr3:53924000-53926400	Active TSS	Colonic Mucosa	Colon
20	chr3:53924200-53925000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:53924200-53925000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:53924200-53925000	Flanking Active TSS	NHDF-Ad	bronchial
23	chr3:53924200-53925200	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr3:53924200-53925200	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr3:53924200-53925200	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr3:53924200-53925200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr3:53924200-53925200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr3:53924200-53925200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr3:53924200-53925200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:53924200-53926600	Active TSS	Psoas Muscle	Psoas
31	chr3:53924200-53926600	Active TSS	Right Atrium	heart
32	chr3:53924200-53926800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:53924400-53925000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr3:53924400-53925000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:53924400-53925000	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr3:53924400-53925000	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr3:53924400-53925000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:53924400-53925000	Flanking Active TSS	HSMM	muscle
39	chr3:53924400-53925000	Flanking Active TSS	NH-A	brain
40	chr3:53924400-53925200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:53924400-53925200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:53924400-53925200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:53924400-53925200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:53924400-53925200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:53924400-53925200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:53924400-53925200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:53924400-53925200	Flanking Active TSS	Fetal Kidney	kidney
48	chr3:53924400-53925400	Flanking Active TSS	Osteobl	bone
49	chr3:53924400-53926400	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:53924400-53926400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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