Variant report

Variant	rs3901406
Chromosome Location	chr9:94896482-94896483
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94896262..94897893-chr9:95004270..95006052,2	K562	blood:
2	chr8:82692841..82693496-chr9:94896066..94896862,2	MCF-7	breast:
3	chr9:94885307..94887334-chr9:94894826..94896515,2	MCF-7	breast:
4	chr2:126952183..126952703-chr9:94896143..94896774,2	MCF-7	breast:
5	chr9:94877231..94877871-chr9:94896353..94897283,2	MCF-7	breast:
6	chr1:202153463..202154431-chr9:94896000..94897129,6	MCF-7	breast:
7	chr9:94896325..94896865-chr9:95396711..95397222,2	K562	blood:
8	chr9:94894716..94897374-chr9:94969241..94971639,2	K562	blood:
9	chr9:94895102..94897917-chr9:95001636..95003511,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000090054	Chromatin interaction
ENSG00000196305	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11787600	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34104615	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62564362	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67451261	0.84[EUR][1000 genomes]
rs7044352	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94894000-94896800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr9:94894800-94897000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr9:94895000-94900200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:94896000-94896600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr9:94896000-94896600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:94896000-94896600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr9:94896000-94896600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr9:94896000-94896600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr9:94896000-94896600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr9:94896000-94896600	Enhancers	Pancreas	Pancrea
11	chr9:94896000-94896600	Active TSS	A549	lung
12	chr9:94896000-94896600	Enhancers	Dnd41	blood
13	chr9:94896000-94896600	Enhancers	K562	blood
14	chr9:94896000-94896600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
15	chr9:94896000-94896800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:94896000-94896800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:94896000-94896800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:94896000-94896800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr9:94896000-94896800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:94896000-94896800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr9:94896000-94896800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:94896000-94896800	Enhancers	Placenta	Placenta
23	chr9:94896000-94896800	Bivalent Enhancer	Fetal Stomach	stomach
24	chr9:94896000-94896800	Enhancers	Right Atrium	heart
25	chr9:94896000-94896800	Enhancers	Right Ventricle	heart
26	chr9:94896000-94896800	Enhancers	HSMMtube	muscle
27	chr9:94896000-94896800	Enhancers	NH-A	brain
28	chr9:94896000-94896800	Flanking Active TSS	Osteobl	bone
29	chr9:94896000-94897000	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr9:94896000-94897000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:94896000-94897000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:94896000-94897000	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr9:94896000-94897200	Enhancers	Ovary	ovary
34	chr9:94896000-94898000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:94896200-94896600	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr9:94896200-94896600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr9:94896200-94896600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr9:94896200-94896600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr9:94896200-94896600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:94896200-94896600	Enhancers	Liver	Liver
41	chr9:94896200-94896600	Active TSS	Brain Substantia Nigra	brain
42	chr9:94896200-94896600	Enhancers	Fetal Brain Female	brain
43	chr9:94896200-94896600	Bivalent Enhancer	Fetal Intestine Small	intestine
44	chr9:94896200-94896600	Enhancers	Fetal Muscle Leg	muscle
45	chr9:94896200-94896600	Enhancers	Gastric	stomach
46	chr9:94896200-94896600	Enhancers	Stomach Mucosa	stomach
47	chr9:94896200-94896600	Enhancers	Spleen	Spleen
48	chr9:94896200-94896600	Active TSS	Hela-S3	cervix
49	chr9:94896200-94896800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:94896200-94896800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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