Variant report

Variant	rs17751980
Chromosome Location	chr14:78067042-78067043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78063987..78068208-chr14:78069326..78072935,4	MCF-7	breast:
2	chr14:78065290..78070188-chr14:78072894..78075904,4	K562	blood:
3	chr14:78064657..78067063-chr14:78079647..78083000,3	MCF-7	breast:
4	chr14:78063505..78065787-chr14:78066559..78069226,2	K562	blood:
5	chr14:78057510..78059603-chr14:78066224..78069062,2	MCF-7	breast:
6	chr14:78064498..78067393-chr14:78068632..78070407,3	K562	blood:
7	chr14:78065290..78068119-chr14:78072066..78074474,3	K562	blood:

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];0.96[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];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176899	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs176906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[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];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176911	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176912	0.94[AMR][1000 genomes];0.96[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751923	0.96[AMR][1000 genomes];0.95[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825014	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]
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];0.99[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];1.00[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];0.96[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];0.96[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];0.87[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];0.96[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
rs17751980	SPTLC2	cis	Nerve Tibial	GTEx
rs17751980	ADCK1	cis	Whole Blood	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
4	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
5	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
7	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
8	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
9	chr14:78056800-78070000	Weak transcription	Gastric	stomach
10	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
11	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr14:78061600-78070000	Weak transcription	Esophagus	oesophagus
14	chr14:78061800-78069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr14:78062200-78068200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:78062200-78070200	Weak transcription	Ovary	ovary
17	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr14:78063200-78070000	Weak transcription	Brain Germinal Matrix	brain
19	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr14:78063400-78069400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:78063400-78069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr14:78063400-78069800	Weak transcription	Liver	Liver
23	chr14:78063400-78070000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr14:78063400-78070200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr14:78063400-78070200	Weak transcription	Fetal Thymus	thymus
26	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
27	chr14:78063600-78067800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr14:78063600-78067800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr14:78063600-78069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr14:78063600-78069600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:78063600-78070200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr14:78063800-78069400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr14:78063800-78071800	Weak transcription	Fetal Lung	lung
34	chr14:78063800-78072000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr14:78063800-78074000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr14:78063800-78074200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:78064400-78067400	Enhancers	A549	lung
38	chr14:78064600-78067400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr14:78064600-78070600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr14:78064800-78067200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr14:78064800-78067200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr14:78064800-78067400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr14:78064800-78067400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr14:78064800-78067400	Enhancers	NHEK	skin
45	chr14:78064800-78067600	Enhancers	Duodenum Mucosa	Duodenum
46	chr14:78065000-78067200	Enhancers	Brain Hippocampus Middle	brain
47	chr14:78065000-78067200	Enhancers	Osteobl	bone
48	chr14:78065000-78067400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:78065000-78068000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr14:78065000-78068000	Enhancers	HSMMtube	muscle

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