Variant report

Variant	rs17825014
Chromosome Location	chr14:78070313-78070314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78069297..78071425-chr14:78081435..78083020,2	K562	blood:
2	chr14:78064498..78067393-chr14:78068632..78070407,3	K562	blood:
3	chr14:78068423..78071899-chr14:78079739..78082860,4	K562	blood:
4	chr14:78069363..78073512-chr14:78081398..78084592,5	MCF-7	breast:
5	chr14:78063987..78068208-chr14:78069326..78072935,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100596	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12431525	0.83[ASN][1000 genomes]
rs12431896	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12433198	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12433954	0.83[ASN][1000 genomes]
rs12434701	0.80[ASN][1000 genomes]
rs12436803	0.83[ASN][1000 genomes]
rs176895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176899	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176908	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176911	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176912	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751876	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17751917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751923	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17752262	1.00[CHB][hapmap]
rs17824984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825229	1.00[CHB][hapmap]
rs17825235	1.00[CHB][hapmap]
rs2142187	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2178877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299918	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2364578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886122	1.00[CHB][hapmap]
rs2886132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35389286	0.83[ASN][1000 genomes]
rs4497612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55697089	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs55776552	1.00[AFR][1000 genomes]
rs55799811	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56264628	1.00[AFR][1000 genomes]
rs56286233	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7159486	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17825014	SPTLC2	cis	Nerve Tibial	GTEx
rs17825014	ADCK1	cis	Whole Blood	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
2	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
3	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
4	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
5	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
9	chr14:78063800-78071800	Weak transcription	Fetal Lung	lung
10	chr14:78063800-78072000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr14:78063800-78074000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr14:78063800-78074200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:78064600-78070600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr14:78065400-78071800	Weak transcription	Thymus	Thymus
15	chr14:78065600-78081400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr14:78065800-78071800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:78066000-78071600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:78066000-78079600	Weak transcription	Dnd41	blood
19	chr14:78066600-78071600	Weak transcription	Fetal Heart	heart
20	chr14:78066600-78074200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr14:78066800-78071400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr14:78066800-78078400	Weak transcription	NHLF	lung
23	chr14:78067000-78078200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr14:78067200-78071400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr14:78067400-78070400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr14:78067800-78070600	Enhancers	NH-A	brain
27	chr14:78067800-78075000	Enhancers	Stomach Mucosa	stomach
28	chr14:78068400-78070600	Enhancers	Brain Hippocampus Middle	brain
29	chr14:78068400-78070600	Enhancers	Osteobl	bone
30	chr14:78068400-78070800	Enhancers	Brain Anterior Caudate	brain
31	chr14:78068400-78071400	Enhancers	NHEK	skin
32	chr14:78068600-78070600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:78068600-78070800	Enhancers	Fetal Kidney	kidney
34	chr14:78068600-78073200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:78069000-78070600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:78069000-78070800	Enhancers	Brain Substantia Nigra	brain
37	chr14:78069000-78070800	Enhancers	HUVEC	blood vessel
38	chr14:78069000-78072800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr14:78069200-78070400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr14:78069200-78072000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr14:78069200-78081600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr14:78069400-78070600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:78069400-78070800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr14:78069400-78070800	Enhancers	Brain Cingulate Gyrus	brain
45	chr14:78069400-78070800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr14:78069400-78071000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr14:78069600-78070400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr14:78069600-78070600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:78069600-78070600	Genic enhancers	HSMM	muscle
50	chr14:78069600-78070600	Enhancers	NHDF-Ad	bronchial

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