Variant report

Variant	rs4417466
Chromosome Location	chr14:21972651-21972652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:21944239..21947571-chr14:21970430..21973821,4	MCF-7	breast:
2	chr14:21972318..21975113-chr14:21978008..21980143,3	K562	blood:

Variant related genes	Relation type
ENSG00000165819	Chromatin interaction
ENSG00000129472	Chromatin interaction
ENSG00000092203	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10450908	0.83[CHB][hapmap]
rs11851342	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1263791	0.83[CEU][hapmap]
rs2242526	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2282046	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3737049	0.80[CEU][hapmap]
rs7144796	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv85879	chr14:21965690-21974198	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4417466	TOX4	Cis_1M	lymphoblastoid	RTeQTL
rs4417466	METTL3	cis	cerebellum	SCAN
rs4417466	METTL3	Cis_1M	lymphoblastoid	RTeQTL
rs4417466	LTB4R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21946200-21977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:21947000-21978000	Weak transcription	Fetal Heart	heart
3	chr14:21954800-21977400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr14:21955600-21977200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:21960400-21973400	Strong transcription	HUVEC	blood vessel
6	chr14:21960600-21973200	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr14:21964000-21977800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:21964800-21973000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr14:21967200-21973200	Strong transcription	Fetal Intestine Small	intestine
10	chr14:21967200-21975800	Strong transcription	HepG2	liver
11	chr14:21967200-21977400	Weak transcription	Small Intestine	intestine
12	chr14:21967400-21973600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr14:21967600-21977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:21967600-21977400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr14:21967800-21974000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr14:21967800-21977200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:21967800-21977400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr14:21967800-21978600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr14:21971600-21975400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr14:21971800-21973200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr14:21971800-21978000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr14:21971800-21978000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr14:21971800-21978200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr14:21971800-21978200	Weak transcription	Stomach Mucosa	stomach
25	chr14:21972000-21972800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr14:21972000-21973000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr14:21972000-21973200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr14:21972000-21973200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr14:21972000-21973200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr14:21972000-21973200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr14:21972000-21973400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr14:21972000-21973800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr14:21972000-21973800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:21972000-21974600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr14:21972000-21974600	Weak transcription	Fetal Stomach	stomach
36	chr14:21972000-21974800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:21972000-21974800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr14:21972000-21974800	Weak transcription	Fetal Muscle Leg	muscle
39	chr14:21972000-21975400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr14:21972000-21975400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr14:21972000-21975400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr14:21972000-21975400	Weak transcription	Fetal Intestine Large	intestine
43	chr14:21972000-21975400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr14:21972000-21975400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr14:21972000-21975400	Weak transcription	HSMMtube	muscle
46	chr14:21972000-21975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr14:21972000-21975600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr14:21972000-21975600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr14:21972000-21975600	Weak transcription	Adipose Nuclei	Adipose
50	chr14:21972000-21975600	Weak transcription	Brain Inferior Temporal Lobe	brain

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