Variant report

Variant	rs72685273
Chromosome Location	chr14:78160115-78160116
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78158386..78160675-chr14:78164018..78166983,2	MCF-7	breast:
2	chr14:78156716..78160622-chr14:78162116..78165748,3	K562	blood:
3	chr14:78154902..78157817-chr14:78159503..78162489,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258917	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10162548	1.00[ASN][1000 genomes]
rs11621162	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621593	0.81[AFR][1000 genomes]
rs11622176	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622293	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622411	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622449	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623898	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624052	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624063	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625029	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625607	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11625647	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11626900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628795	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752726	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825620	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032745	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111829	0.81[AMR][1000 genomes]
rs2112135	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445066	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28541608	1.00[ASN][1000 genomes]
rs28607620	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28651563	0.90[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	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45465691	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4996830	1.00[ASN][1000 genomes]
rs55636050	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55922310	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55995783	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003103	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025136	0.88[ASN][1000 genomes]
rs56060413	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56065232	1.00[ASN][1000 genomes]
rs56109335	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56339806	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57615727	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58171071	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59200674	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493	0.92[AFR][1000 genomes]
rs6494	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146719	1.00[ASN][1000 genomes]
rs7148685	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155062	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685214	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685216	0.90[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	0.92[AFR][1000 genomes]
rs72685244	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685246	0.92[AFR][1000 genomes]
rs72685260	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685280	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685293	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685296	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685297	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72685300	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685302	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687205	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687217	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687218	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687222	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687223	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72687228	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687229	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687246	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687247	0.81[AFR][1000 genomes]
rs72687250	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687251	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687261	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688824	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7492501	0.81[AFR][1000 genomes]
rs8015313	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	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	nsv869872	chr14:78119527-78161340	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	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
rs72685273	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 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	chr14:78134400-78163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:78136200-78162800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:78137800-78161200	Weak transcription	Fetal Heart	heart
5	chr14:78138000-78171800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr14:78140400-78160400	Weak transcription	Fetal Kidney	kidney
7	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:78141200-78160400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:78141200-78162800	Weak transcription	Colonic Mucosa	Colon
11	chr14:78142200-78161200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr14:78142600-78162200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:78142600-78162800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:78146400-78161800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr14:78148400-78162800	Weak transcription	Aorta	Aorta
16	chr14:78148400-78162800	Weak transcription	Pancreas	Pancrea
17	chr14:78148400-78164400	Weak transcription	Psoas Muscle	Psoas
18	chr14:78148600-78162800	Weak transcription	NHLF	lung
19	chr14:78149000-78160400	Weak transcription	Hela-S3	cervix
20	chr14:78149200-78163800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr14:78149200-78171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:78149800-78163000	Weak transcription	Stomach Mucosa	stomach
23	chr14:78149800-78164200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr14:78150200-78163800	Strong transcription	Fetal Muscle Leg	muscle
25	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:78152200-78164200	Strong transcription	Liver	Liver
27	chr14:78152200-78164600	Strong transcription	Adipose Nuclei	Adipose
28	chr14:78152400-78171200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:78152800-78165400	Strong transcription	Placenta	Placenta
31	chr14:78152800-78171400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr14:78153400-78163000	Weak transcription	Right Ventricle	heart
33	chr14:78153400-78171200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr14:78153400-78171400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr14:78154400-78162600	Weak transcription	HSMMtube	muscle
37	chr14:78154400-78168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr14:78154400-78172600	Weak transcription	Small Intestine	intestine
39	chr14:78154600-78167200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr14:78155400-78163600	Strong transcription	HSMM	muscle
41	chr14:78155400-78163800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:78155600-78163800	Strong transcription	Fetal Brain Female	brain
43	chr14:78155600-78164000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:78155600-78164800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr14:78155800-78163800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:78155800-78165600	Strong transcription	Primary T cells from cord blood	blood
47	chr14:78156000-78171400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr14:78156200-78160800	Strong transcription	GM12878-XiMat	blood
49	chr14:78156200-78163800	Strong transcription	Fetal Thymus	thymus
50	chr14:78156200-78164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links