Variant report

Variant	rs1964842
Chromosome Location	chr14:39565453-39565454
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	chr14:39564253..39566731-chr14:39570082..39573549,3	MCF-7	breast:
2	chr14:39565337..39567780-chr14:39737837..39739519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258651	Chromatin interaction
ENSG00000100934	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10132034	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10132953	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10149829	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11157046	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11157047	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11157048	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12434607	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12895329	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175341	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1950509	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1955917	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1956629	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2038357	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2082637	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2180214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2180217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180792	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2252040	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2415531	0.81[EUR][1000 genomes]
rs3899404	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4290398	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4616209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4899139	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4899140	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902294	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902402	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902419	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56163817	0.81[ASN][1000 genomes]
rs6571888	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6571889	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6571890	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6571891	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6571894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6571895	0.93[AMR][1000 genomes]
rs6571896	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7147760	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154585	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7157204	0.86[AMR][1000 genomes]
rs761804	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs761806	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs761807	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8003194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8003485	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8003807	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8010111	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8011855	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8012178	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8014255	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8014677	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8022141	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9322993	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9671927	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs970623	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs975591	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39525600-39565600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr14:39526800-39566600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr14:39528000-39565600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr14:39528600-39566400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:39529200-39566600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr14:39529800-39566400	Weak transcription	Fetal Heart	heart
7	chr14:39531200-39569200	Weak transcription	Stomach Mucosa	stomach
8	chr14:39534200-39566600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr14:39534600-39566800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:39538600-39566400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr14:39539000-39566600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr14:39549200-39565600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr14:39549200-39565600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr14:39554200-39571200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:39554800-39571600	Weak transcription	K562	blood
16	chr14:39555200-39571600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:39555800-39569000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr14:39556800-39566200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr14:39556800-39566800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr14:39557200-39566400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr14:39558400-39566000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr14:39558600-39565600	Strong transcription	Dnd41	blood
23	chr14:39558600-39566000	Strong transcription	A549	lung
24	chr14:39558800-39571400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr14:39560200-39565600	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:39560200-39566000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr14:39560200-39566400	Weak transcription	Small Intestine	intestine
28	chr14:39560200-39569400	Weak transcription	Spleen	Spleen
29	chr14:39560200-39569800	Weak transcription	Pancreas	Pancrea
30	chr14:39560200-39571000	Weak transcription	Aorta	Aorta
31	chr14:39560400-39571400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr14:39560400-39571600	Weak transcription	Esophagus	oesophagus
33	chr14:39560400-39571600	Weak transcription	Gastric	stomach
34	chr14:39561000-39565800	Strong transcription	Fetal Intestine Large	intestine
35	chr14:39561000-39566400	Weak transcription	Right Ventricle	heart
36	chr14:39561000-39570600	Weak transcription	Lung	lung
37	chr14:39561000-39571200	Weak transcription	Colonic Mucosa	Colon
38	chr14:39561000-39571400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr14:39561000-39571400	Weak transcription	Psoas Muscle	Psoas
40	chr14:39561400-39565600	Strong transcription	Left Ventricle	heart
41	chr14:39561400-39566200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr14:39561400-39569200	Weak transcription	Fetal Brain Male	brain
43	chr14:39561600-39565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr14:39561600-39566200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr14:39561600-39569000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:39561600-39571200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr14:39561600-39571400	Weak transcription	Brain Hippocampus Middle	brain
48	chr14:39561600-39571600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr14:39562000-39566000	Strong transcription	Fetal Intestine Small	intestine
50	chr14:39562200-39565600	Strong transcription	Fetal Stomach	stomach

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