Variant report

Variant	rs11623642
Chromosome Location	chr14:21855880-21855881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr14:21855640-21855934	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:21851475..21856107-chr14:21857808..21863193,8	K562	blood:
2	chr14:21854245..21857483-chr14:21860851..21864599,3	MCF-7	breast:
3	chr14:21848861..21852877-chr14:21854432..21859173,7	MCF-7	breast:

Variant related genes	Relation type
SUPT16H	TF binding region
CHD8	TF binding region
ENSG00000260830	Chromatin interaction
ENSG00000199436	Chromatin interaction
ENSG00000092201	Chromatin interaction
ENSG00000100888	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1008268	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1008269	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10132333	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10134108	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10135022	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10137743	0.83[AMR][1000 genomes]
rs10138699	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10139379	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10143061	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10146717	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10150329	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10151764	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1045842	0.80[AMR][1000 genomes]
rs10782384	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11623599	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11623737	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11624716	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12885503	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1543494	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1952554	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1983768	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1998330	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1998331	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1998332	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1999139	0.80[AMR][1000 genomes]
rs2007434	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2065096	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2146062	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2149749	0.81[AMR][1000 genomes]
rs2181125	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2295865	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2295866	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3762156	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762157	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762158	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762159	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4144189	0.83[AMR][1000 genomes]
rs4246991	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4982445	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982446	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6571770	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6571797	0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6571826	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7147024	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7148741	0.91[ASN][1000 genomes]
rs7152833	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7155123	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7160488	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8004294	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8004388	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8007893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8008670	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8009789	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8011945	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8017451	0.84[AMR][1000 genomes]
rs8017630	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8018369	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8020149	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8022395	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022755	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs927412	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv916319	chr14:21507092-21896590	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1043570	chr14:21575068-21899964	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv541977	chr14:21575068-21899964	Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	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
9	nsv1044822	chr14:21659344-21860081	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv1051407	chr14:21692670-21907366	Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv541984	chr14:21692670-21907366	Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	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
13	nsv428617	chr14:21721165-21871164	Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11623642	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	chr14:21853000-21856200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:21853000-21856600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:21853000-21859600	Weak transcription	Fetal Brain Male	brain
4	chr14:21853000-21865000	Weak transcription	Stomach Mucosa	stomach
5	chr14:21853000-21868000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:21853200-21856000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr14:21853200-21856400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr14:21853200-21857600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr14:21853200-21860200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr14:21853200-21860600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr14:21853200-21863800	Weak transcription	Right Atrium	heart
12	chr14:21853200-21865400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr14:21853200-21884400	Strong transcription	NH-A	brain
14	chr14:21853200-21904000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:21853400-21856800	Weak transcription	Brain Hippocampus Middle	brain
16	chr14:21853400-21856800	Weak transcription	A549	lung
17	chr14:21853400-21857000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr14:21853400-21857600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr14:21853400-21858000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:21853400-21859200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr14:21853400-21859600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr14:21853400-21860000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr14:21853400-21860600	Weak transcription	Fetal Heart	heart
24	chr14:21853400-21875800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:21853400-21876000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:21853400-21876200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:21853400-21876200	Strong transcription	Osteobl	bone
28	chr14:21853400-21876400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:21853400-21877800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:21853400-21879800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr14:21853400-21884200	Strong transcription	Colon Smooth Muscle	Colon
32	chr14:21853400-21884400	Strong transcription	Fetal Muscle Leg	muscle
33	chr14:21853400-21884800	Strong transcription	Fetal Brain Female	brain
34	chr14:21853400-21900000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:21853400-21900000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr14:21853400-21900000	Strong transcription	Adipose Nuclei	Adipose
37	chr14:21853400-21900000	Strong transcription	Placenta	Placenta
38	chr14:21853400-21900200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:21853400-21901800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr14:21853600-21856600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr14:21853600-21856600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:21853600-21876800	Strong transcription	Fetal Stomach	stomach
43	chr14:21853600-21884000	Strong transcription	Brain Substantia Nigra	brain
44	chr14:21853600-21884400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr14:21853600-21884400	Strong transcription	HSMM	muscle
46	chr14:21853600-21885000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr14:21853600-21885800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr14:21853600-21886800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr14:21853600-21888800	Strong transcription	Fetal Intestine Large	intestine
50	chr14:21853600-21897200	Strong transcription	Fetal Muscle Trunk	muscle

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