Variant report

Variant	rs72685281
Chromosome Location	chr14:78169618-78169619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78166641..78172350-chr14:78172652..78176323,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10162548	1.00[ASN][1000 genomes]
rs11621162	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621593	0.87[AFR][1000 genomes]
rs11622176	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752726	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111829	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2112135	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461000	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464012	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45444693	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[ASN][1000 genomes]
rs55636050	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56060413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339806	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57615727	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493	0.87[AFR][1000 genomes]
rs6494	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[ASN][1000 genomes]
rs7148685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685216	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685219	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685222	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685223	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685230	1.00[ASN][1000 genomes]
rs72685232	1.00[ASN][1000 genomes]
rs72685238	0.87[AFR][1000 genomes]
rs72685244	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685246	0.87[AFR][1000 genomes]
rs72685260	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685297	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72685300	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685302	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687205	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687223	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687228	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687247	0.87[AFR][1000 genomes]
rs72687250	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687251	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8015313	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72685281	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78138000-78171800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:78149200-78171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:78152400-78171200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:78152800-78171400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr14:78153400-78171200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr14:78153400-78171400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr14:78154400-78172600	Weak transcription	Small Intestine	intestine
14	chr14:78156000-78171400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr14:78156200-78172000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr14:78156600-78171800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr14:78156800-78170000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr14:78156800-78171400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr14:78156800-78172400	Strong transcription	Dnd41	blood
20	chr14:78158600-78172800	Weak transcription	NHDF-Ad	bronchial
21	chr14:78162600-78171400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr14:78163600-78170200	Weak transcription	Fetal Kidney	kidney
23	chr14:78163600-78170600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr14:78163800-78170200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr14:78163800-78170200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:78163800-78170200	Weak transcription	Fetal Brain Male	brain
27	chr14:78163800-78170400	Weak transcription	NH-A	brain
28	chr14:78163800-78170400	Weak transcription	NHLF	lung
29	chr14:78163800-78170600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:78163800-78172600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr14:78163800-78172600	Weak transcription	HMEC	breast
32	chr14:78163800-78173400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:78163800-78173400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr14:78163800-78173400	Weak transcription	Right Ventricle	heart
35	chr14:78164000-78173000	Weak transcription	HSMMtube	muscle
36	chr14:78164000-78173400	Weak transcription	Aorta	Aorta
37	chr14:78164200-78170200	Weak transcription	HepG2	liver
38	chr14:78165200-78170400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr14:78165400-78171000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:78165400-78171200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:78165600-78171200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr14:78165800-78172600	Weak transcription	Fetal Heart	heart
43	chr14:78166000-78170200	Weak transcription	Colon Smooth Muscle	Colon
44	chr14:78166000-78170400	Weak transcription	K562	blood
45	chr14:78166400-78171800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr14:78166400-78172200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr14:78166400-78172800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr14:78166600-78171200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:78166600-78171200	Strong transcription	Primary B cells from cord blood	blood
50	chr14:78166600-78171400	Strong transcription	Brain Inferior Temporal Lobe	brain

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