Variant report

Variant	rs3964454
Chromosome Location	chr3:196357362-196357363
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196342656..196345051-chr3:196357362..196359188,2	K562	blood:
2	chr3:196353912..196357816-chr3:196358076..196361478,4	MCF-7	breast:
3	chr3:196321228..196324208-chr3:196356840..196359377,2	K562	blood:
4	chr3:196356860..196359000-chr3:196386033..196388498,2	K562	blood:
5	chr3:196355388..196357722-chr3:196358115..196360869,2	MCF-7	breast:
6	chr3:196250394..196252273-chr3:196357223..196359043,2	K562	blood:
7	chr3:196356110..196358354-chr3:196361482..196363401,2	MCF-7	breast:
8	chr3:196332639..196334602-chr3:196356854..196359428,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12718061	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12718062	0.98[ASN][1000 genomes]
rs1385331	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34088166	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34515026	0.96[ASN][1000 genomes]
rs6583331	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6799977	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807839	0.94[ASN][1000 genomes]
rs7614184	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9824819	0.82[ASN][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	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv1003135	chr3:196348721-196738953	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196347600-196358200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:196347600-196358400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:196347600-196358400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:196347600-196358400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:196350600-196358600	Weak transcription	Lung	lung
6	chr3:196350600-196358600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:196351400-196358400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:196351400-196358800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:196351600-196357600	Weak transcription	K562	blood
10	chr3:196351600-196358400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:196351600-196358600	Weak transcription	Brain Angular Gyrus	brain
12	chr3:196351600-196358600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:196351800-196358400	Enhancers	Fetal Thymus	thymus
14	chr3:196352000-196358000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:196352000-196358800	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:196352200-196358400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:196352200-196358600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:196352400-196358200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr3:196352400-196358600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:196352400-196358600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:196352400-196358600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:196352400-196358800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:196352600-196358000	Weak transcription	Primary B cells from cord blood	blood
24	chr3:196354200-196358400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:196354200-196358400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:196354200-196358600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:196354200-196358600	Weak transcription	Osteobl	bone
28	chr3:196354600-196358600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:196354800-196358200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:196354800-196358400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:196354800-196358400	Weak transcription	A549	lung
32	chr3:196354800-196358600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:196355000-196358600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:196355000-196358600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:196355000-196358600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:196355000-196358600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:196355200-196358200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:196355200-196358200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:196355200-196358400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:196355200-196358400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:196355200-196358400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:196355200-196358400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:196355200-196358400	Weak transcription	Hela-S3	cervix
44	chr3:196355200-196358600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:196355200-196358600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:196355200-196358600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:196355200-196358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:196355200-196358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:196355400-196358200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:196355800-196357800	Enhancers	Dnd41	blood

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