Variant report

Variant	rs16958889
Chromosome Location	chr16:69499536-69499537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69494261..69496702-chr16:69498407..69501487,3	K562	blood:
2	chr16:69491057..69494672-chr16:69499045..69501643,3	K562	blood:
3	chr16:69495315..69497830-chr16:69499149..69500993,2	MCF-7	breast:
4	chr16:69469350..69472024-chr16:69498494..69500760,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NFAT5-2	chr16:69497747-69500167	ENSG00000260108.1

Variant related genes	Relation type
ENSG00000260108	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11859488	1.00[AMR][1000 genomes]
rs11860750	1.00[AMR][1000 genomes]
rs11861496	1.00[AMR][1000 genomes]
rs11861500	1.00[AMR][1000 genomes]
rs11862202	1.00[AMR][1000 genomes]
rs11864406	1.00[AMR][1000 genomes]
rs11864525	1.00[AMR][1000 genomes]
rs11865019	1.00[AMR][1000 genomes]
rs11866304	1.00[AMR][1000 genomes]
rs16958892	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28525492	1.00[AMR][1000 genomes]
rs61730073	1.00[AMR][1000 genomes]
rs6499233	1.00[AMR][1000 genomes]
rs6499235	1.00[AMR][1000 genomes]
rs6499236	1.00[AMR][1000 genomes]
rs6499242	1.00[AMR][1000 genomes]
rs7185430	1.00[AMR][1000 genomes]
rs7186199	1.00[AMR][1000 genomes]
rs7187272	1.00[AMR][1000 genomes]
rs7188149	1.00[AMR][1000 genomes]
rs7190711	1.00[AMR][1000 genomes]
rs7195974	1.00[AMR][1000 genomes]
rs7196193	1.00[AMR][1000 genomes]
rs7199248	1.00[AMR][1000 genomes]
rs7204285	1.00[AMR][1000 genomes]
rs74025775	1.00[AMR][1000 genomes]
rs8047310	1.00[AMR][1000 genomes]
rs8049055	1.00[AMR][1000 genomes]
rs8052967	1.00[AMR][1000 genomes]
rs8054678	1.00[AMR][1000 genomes]
rs8056135	1.00[AMR][1000 genomes]
rs8059310	1.00[AMR][1000 genomes]
rs8059804	1.00[AMR][1000 genomes]
rs8060543	1.00[AMR][1000 genomes]
rs9746717	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064808	chr16:69271190-69552951	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv542940	chr16:69271190-69552951	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69459400-69500600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:69473400-69501600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:69473800-69499600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:69478400-69503200	Weak transcription	Spleen	Spleen
5	chr16:69479200-69501400	Weak transcription	Aorta	Aorta
6	chr16:69479400-69503600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr16:69479600-69517600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr16:69479800-69505000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:69480600-69501200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr16:69481400-69503800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr16:69481600-69500800	Weak transcription	Ovary	ovary
12	chr16:69482800-69500800	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:69483000-69501400	Weak transcription	Psoas Muscle	Psoas
14	chr16:69483000-69503600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr16:69483000-69505600	Weak transcription	Right Ventricle	heart
16	chr16:69483600-69503600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr16:69484000-69508200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr16:69487800-69500600	Strong transcription	Dnd41	blood
19	chr16:69489800-69510800	Weak transcription	Right Atrium	heart
20	chr16:69494200-69510800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:69496400-69500400	Strong transcription	Fetal Muscle Leg	muscle
22	chr16:69496800-69501200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr16:69497000-69500800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr16:69497000-69501600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:69497200-69499800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr16:69497200-69500400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:69497200-69502400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr16:69497200-69504000	Weak transcription	Esophagus	oesophagus
29	chr16:69497200-69504000	Weak transcription	Lung	lung
30	chr16:69497200-69510800	Weak transcription	Gastric	stomach
31	chr16:69497400-69500000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr16:69497400-69500200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:69497400-69500200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr16:69497400-69502000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr16:69497600-69499800	Weak transcription	Fetal Brain Male	brain
36	chr16:69497600-69500000	Enhancers	Brain Hippocampus Middle	brain
37	chr16:69497600-69500200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr16:69497600-69501400	Enhancers	Brain Angular Gyrus	brain
39	chr16:69497600-69502000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr16:69497800-69499600	Enhancers	Duodenum Mucosa	Duodenum
41	chr16:69497800-69499800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr16:69497800-69500000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr16:69497800-69500000	Enhancers	Fetal Lung	lung
44	chr16:69497800-69500200	Enhancers	Brain Substantia Nigra	brain
45	chr16:69497800-69500400	Enhancers	Osteobl	bone
46	chr16:69497800-69501400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr16:69497800-69501400	Enhancers	Brain Anterior Caudate	brain
48	chr16:69497800-69510800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr16:69498000-69499600	Weak transcription	Fetal Brain Female	brain
50	chr16:69498000-69499800	Enhancers	Primary T helper cells fromperipheralblood	blood

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