Variant report

Variant	rs2142187
Chromosome Location	chr14:78057835-78057836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78050054..78053077-chr14:78055760..78058382,3	K562	blood:
2	chr14:78051627..78054130-chr14:78057601..78060266,3	MCF-7	breast:
3	chr14:78057510..78059603-chr14:78066224..78069062,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12431896	0.85[JPT][hapmap]
rs12433198	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12433737	0.84[ASN][1000 genomes]
rs176895	0.86[ASN][1000 genomes]
rs176896	0.86[ASN][1000 genomes]
rs176906	0.86[ASN][1000 genomes]
rs176908	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs176911	0.86[ASN][1000 genomes]
rs176912	0.86[ASN][1000 genomes]
rs17751876	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs17751917	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17751923	0.93[ASN][1000 genomes]
rs17751980	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17751993	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17824984	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17825014	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2178877	0.93[ASN][1000 genomes]
rs2299918	0.84[ASN][1000 genomes]
rs2364578	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2886132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4497612	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7159486	0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2142187	SPTLC2	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:78016400-78061000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr14:78021800-78061000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:78022000-78060800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:78042400-78059000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:78042400-78060800	Weak transcription	Aorta	Aorta
10	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
11	chr14:78042600-78061800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr14:78043000-78059800	Weak transcription	A549	lung
13	chr14:78043200-78058800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr14:78043800-78060800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr14:78043800-78061000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr14:78043800-78061200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr14:78043800-78061800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:78044000-78060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:78044000-78061000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr14:78044000-78061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr14:78044600-78061000	Weak transcription	Thymus	Thymus
22	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
23	chr14:78047600-78059600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr14:78047800-78059800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:78047800-78061000	Weak transcription	Brain Germinal Matrix	brain
26	chr14:78048000-78059800	Weak transcription	K562	blood
27	chr14:78048000-78061400	Weak transcription	Fetal Intestine Small	intestine
28	chr14:78048200-78059600	Weak transcription	NH-A	brain
29	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
30	chr14:78049200-78059600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr14:78049200-78059800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr14:78049400-78059600	Weak transcription	Osteobl	bone
33	chr14:78049400-78059800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr14:78049400-78060800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:78049400-78061000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr14:78049600-78061000	Weak transcription	Fetal Muscle Leg	muscle
38	chr14:78050800-78061000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:78051400-78059600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:78051400-78061400	Weak transcription	Esophagus	oesophagus
41	chr14:78051400-78061800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr14:78051400-78061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr14:78051400-78066200	Weak transcription	Pancreas	Pancrea
44	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr14:78051600-78060000	Weak transcription	Fetal Lung	lung
46	chr14:78051600-78060800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr14:78051600-78060800	Weak transcription	Fetal Stomach	stomach
48	chr14:78051600-78060800	Weak transcription	HSMMtube	muscle
49	chr14:78051600-78061000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr14:78051600-78063000	Weak transcription	Left Ventricle	heart

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