Variant report

Variant	rs1999139
Chromosome Location	chr14:21923547-21923548
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:21876017..21878615-chr14:21922957..21924829,2	MCF-7	breast:
2	chr14:21895846..21897870-chr14:21921623..21924084,2	K562	blood:
3	chr14:21923260..21925455-chr14:21943748..21947334,4	K562	blood:
4	chr14:21896024..21898915-chr14:21922681..21926768,3	MCF-7	breast:
5	chr14:21903062..21910356-chr14:21920914..21926084,11	K562	blood:
6	chr14:21903199..21908176-chr14:21922150..21927422,17	MCF-7	breast:
7	chr14:21895886..21898457-chr14:21923417..21926008,3	MCF-7	breast:
8	chr14:21922721..21925394-chr14:21943917..21947287,10	MCF-7	breast:
9	chr14:21850281..21853606-chr14:21922401..21926243,8	K562	blood:
10	chr14:21850843..21852612-chr14:21923284..21925387,2	MCF-7	breast:
11	chr14:21904171..21908174-chr14:21922677..21925847,6	K562	blood:
12	chr14:21902087..21907117-chr14:21919849..21925728,16	MCF-7	breast:
13	chr14:21922608..21930261-chr14:21941288..21947915,21	MCF-7	breast:
14	chr14:21923462..21925701-chr14:21977921..21979566,3	MCF-7	breast:
15	chr14:21923226..21926054-chr6:27860528..27862245,2	MCF-7	breast:
16	chr14:21921735..21926252-chr14:21977495..21980798,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260830	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000129472	Chromatin interaction
ENSG00000092201	Chromatin interaction
ENSG00000092203	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000165819	Chromatin interaction
ENSG00000263621	Chromatin interaction
ENSG00000100888	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1008268	0.80[AMR][1000 genomes]
rs10132333	0.83[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes]
rs10134108	0.82[MEX][hapmap]
rs10135022	0.85[AMR][1000 genomes]
rs10139379	0.82[AMR][1000 genomes]
rs10141933	0.89[EUR][1000 genomes]
rs10142478	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10143000	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs10143061	0.83[GIH][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs10146717	0.82[MEX][hapmap]
rs10150329	0.82[AMR][1000 genomes]
rs1045842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11156996	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11623642	0.80[AMR][1000 genomes]
rs11624716	0.82[MEX][hapmap]
rs1263788	0.91[EUR][1000 genomes]
rs1263790	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs1263792	1.00[ASW][hapmap];0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1263797	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1263798	0.89[EUR][1000 genomes]
rs1543494	0.82[MEX][hapmap]
rs1794219	0.89[EUR][1000 genomes]
rs1998332	0.82[MEX][hapmap]
rs2007434	0.82[AMR][1000 genomes]
rs2065096	0.80[AMR][1000 genomes]
rs2146062	0.82[AMR][1000 genomes]
rs2295865	0.84[AMR][1000 genomes]
rs3762156	0.82[AMR][1000 genomes]
rs3762157	0.85[AMR][1000 genomes]
rs3762158	0.83[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs3762159	0.82[MEX][hapmap]
rs3762162	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap]
rs4144189	0.82[JPT][hapmap]
rs4982445	0.85[AMR][1000 genomes]
rs6571770	0.85[AMR][1000 genomes]
rs6571797	0.82[MEX][hapmap]
rs6571826	0.80[AMR][1000 genomes]
rs6571843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs6571845	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs6571846	0.86[CHB][hapmap]
rs6571856	0.84[EUR][1000 genomes]
rs7141654	0.89[CHB][hapmap]
rs7151259	0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs7152833	0.83[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs7157961	0.89[EUR][1000 genomes]
rs7159433	0.94[EUR][1000 genomes]
rs7160488	0.82[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs8004388	0.83[GIH][hapmap];0.82[MEX][hapmap]
rs8005163	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap]
rs8007893	0.80[AMR][1000 genomes]
rs8008670	0.82[CEU][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs8009789	0.83[GIH][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes]
rs8017630	0.80[AMR][1000 genomes]
rs8018369	0.82[AMR][1000 genomes]
rs8020149	0.82[AMR][1000 genomes]
rs8022395	0.83[GIH][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs8022755	0.82[AMR][1000 genomes]
rs927412	0.85[AMR][1000 genomes]
rs9322978	0.88[MEX][hapmap]

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	nsv948957	chr14:21616875-21928338	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv530010	chr14:21692670-21923767	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1999139	TOX4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21922000-21925000	Active TSS	GM12878-XiMat	blood
2	chr14:21922400-21923600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr14:21922400-21923600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr14:21922400-21923600	Flanking Active TSS	Dnd41	blood
5	chr14:21922400-21923800	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr14:21922400-21925000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr14:21922400-21925200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr14:21922400-21925200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr14:21922600-21923600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr14:21922600-21923600	Flanking Active TSS	Fetal Brain Male	brain
11	chr14:21922600-21925000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:21922800-21923600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:21922800-21923600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr14:21922800-21923600	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr14:21922800-21923600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr14:21922800-21923600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr14:21922800-21923600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr14:21922800-21923600	Flanking Active TSS	Hela-S3	cervix
19	chr14:21922800-21923600	Flanking Active TSS	Osteobl	bone
20	chr14:21922800-21923800	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr14:21922800-21923800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr14:21922800-21923800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr14:21922800-21923800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr14:21922800-21923800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr14:21922800-21923800	Flanking Active TSS	Fetal Brain Female	brain
26	chr14:21922800-21924000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr14:21922800-21925000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr14:21922800-21925000	Active TSS	K562	blood
29	chr14:21922800-21925000	Active TSS	NHLF	lung
30	chr14:21922800-21925200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:21922800-21925200	Active TSS	Fetal Intestine Large	intestine
32	chr14:21923000-21923600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr14:21923000-21923600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:21923000-21923600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr14:21923000-21923600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr14:21923000-21923600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:21923000-21923600	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr14:21923000-21923600	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr14:21923000-21923600	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr14:21923000-21923600	Flanking Active TSS	Colonic Mucosa	Colon
41	chr14:21923000-21923600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr14:21923000-21923600	Flanking Active TSS	Fetal Lung	lung
43	chr14:21923000-21923600	Flanking Active TSS	Fetal Thymus	thymus
44	chr14:21923000-21923600	Flanking Active TSS	Stomach Mucosa	stomach
45	chr14:21923000-21923600	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr14:21923000-21923600	Flanking Active TSS	Thymus	Thymus
47	chr14:21923000-21923600	Flanking Active TSS	HUVEC	blood vessel
48	chr14:21923000-21923600	Flanking Active TSS	NH-A	brain
49	chr14:21923000-21923800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr14:21923000-21923800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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