Variant report

Variant	rs2100489
Chromosome Location	chr14:69931254-69931255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10129720	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10140273	0.92[AMR][1000 genomes]
rs10143593	0.81[AMR][1000 genomes]
rs10143710	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10151691	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11622711	0.82[AMR][1000 genomes]
rs11623094	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11624577	0.81[AMR][1000 genomes]
rs12147478	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12147967	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12436172	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12878175	0.81[AMR][1000 genomes]
rs12891351	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12893282	0.85[AMR][1000 genomes]
rs1466255	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1958121	0.81[AMR][1000 genomes]
rs1965878	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2124192	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296722	0.82[AMR][1000 genomes]
rs28879441	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34405286	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34450502	0.90[AMR][1000 genomes]
rs34840252	0.81[AMR][1000 genomes]
rs3759770	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4899295	0.80[AMR][1000 genomes]
rs4902719	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56392460	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56953348	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7145944	0.82[AMR][1000 genomes]
rs7147362	0.81[AMR][1000 genomes]
rs7147710	0.81[AMR][1000 genomes]
rs7150586	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7160248	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8010767	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8012954	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8014890	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8016781	0.81[AMR][1000 genomes]
rs8020817	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9796392	0.89[AMR][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	esv3396933	chr14:69906914-70001258	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1048882	chr14:69920881-69976694	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052107	chr14:69922552-69969297	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1039230	chr14:69922552-69972002	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1039192	chr14:69922552-69976694	Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv456335	chr14:69928307-69971598	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv564967	chr14:69928307-69971598	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2100489	SLC39A9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69892200-69931400	Weak transcription	K562	blood
2	chr14:69903600-69937800	Weak transcription	Psoas Muscle	Psoas
3	chr14:69909000-69933200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr14:69915800-69932600	Weak transcription	Fetal Heart	heart
5	chr14:69922200-69931600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:69923600-69950400	Weak transcription	Gastric	stomach
7	chr14:69924200-69931400	Weak transcription	Small Intestine	intestine
8	chr14:69925400-69931400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr14:69925400-69939600	Weak transcription	Pancreas	Pancrea
10	chr14:69925400-69942000	Weak transcription	Spleen	Spleen
11	chr14:69925600-69940000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:69925600-69940000	Weak transcription	Hela-S3	cervix
13	chr14:69926000-69931400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:69926000-69933000	Weak transcription	A549	lung
15	chr14:69926000-69933200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr14:69926000-69940000	Weak transcription	Brain Anterior Caudate	brain
17	chr14:69926000-69940000	Weak transcription	Fetal Intestine Small	intestine
18	chr14:69926200-69935200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr14:69926200-69937200	Weak transcription	Left Ventricle	heart
20	chr14:69927800-69939400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:69928000-69932600	Weak transcription	Fetal Stomach	stomach
22	chr14:69928000-69933600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr14:69928000-69941000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr14:69928400-69934400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr14:69928600-69932800	Weak transcription	GM12878-XiMat	blood
26	chr14:69928600-69935000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr14:69928600-69950600	Weak transcription	Aorta	Aorta
28	chr14:69928800-69931400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:69928800-69933400	Weak transcription	Fetal Thymus	thymus
30	chr14:69928800-69940200	Weak transcription	Thymus	Thymus
31	chr14:69928800-69940400	Weak transcription	Adipose Nuclei	Adipose
32	chr14:69928800-69941000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr14:69929000-69933200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr14:69929000-69933200	Weak transcription	Dnd41	blood
35	chr14:69929000-69933400	Weak transcription	Primary B cells from cord blood	blood
36	chr14:69929000-69934000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr14:69929000-69934200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr14:69929000-69935200	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr14:69929000-69935800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr14:69929000-69938800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr14:69929000-69940200	Weak transcription	HSMMtube	muscle
42	chr14:69929000-69940400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:69929000-69941400	Weak transcription	Ovary	ovary
44	chr14:69929200-69931400	Weak transcription	HSMM	muscle
45	chr14:69929200-69933400	Weak transcription	Primary T cells from cord blood	blood
46	chr14:69929200-69935800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr14:69929400-69931400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr14:69929400-69932600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:69929400-69933000	Weak transcription	Fetal Intestine Large	intestine
50	chr14:69929400-69933200	Weak transcription	Fetal Brain Female	brain

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