Variant report

Variant	rs176895
Chromosome Location	chr14:78074806-78074807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78065290..78070188-chr14:78072894..78075904,4	K562	blood:
2	chr14:78072044..78075600-chr14:78081551..78084450,6	K562	blood:
3	chr14:78072993..78075148-chr14:78173100..78175797,2	K562	blood:
4	chr14:78072769..78075588-chr14:78081350..78084450,3	K562	blood:
5	chr14:78071276..78074499-chr14:78074506..78077837,3	K562	blood:

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000119705	Chromatin interaction
ENSG00000100596	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12431525	0.90[ASN][1000 genomes]
rs12431896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12433198	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12433954	0.90[ASN][1000 genomes]
rs12434701	0.87[ASN][1000 genomes]
rs12436803	0.90[ASN][1000 genomes]
rs176896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176899	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176906	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176908	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176911	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176912	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751876	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17751917	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751923	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751980	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751993	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17824984	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17825014	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2142187	0.86[ASN][1000 genomes]
rs2178877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299918	0.81[AMR][1000 genomes]
rs2364578	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886132	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35389286	0.90[ASN][1000 genomes]
rs4497612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55697089	1.00[AFR][1000 genomes]
rs55776552	1.00[AFR][1000 genomes]
rs55799811	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56264628	1.00[AFR][1000 genomes]
rs56286233	1.00[AFR][1000 genomes]
rs58312042	0.84[ASN][1000 genomes]
rs59721556	0.84[ASN][1000 genomes]
rs7159486	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs176895	SPTLC2	cis	Nerve Tibial	GTEx
rs176895	ADCK1	cis	Whole Blood	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
2	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
6	chr14:78065600-78081400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr14:78066000-78079600	Weak transcription	Dnd41	blood
8	chr14:78066800-78078400	Weak transcription	NHLF	lung
9	chr14:78067000-78078200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr14:78067800-78075000	Enhancers	Stomach Mucosa	stomach
11	chr14:78069200-78081600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr14:78070000-78075600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr14:78070200-78081600	Weak transcription	Liver	Liver
14	chr14:78070400-78075000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr14:78070400-78075800	Weak transcription	Lung	lung
16	chr14:78070400-78078200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr14:78070400-78078400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr14:78070400-78079800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:78070400-78081400	Weak transcription	Fetal Muscle Leg	muscle
20	chr14:78070600-78076800	Weak transcription	HSMM	muscle
21	chr14:78070600-78077800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr14:78070600-78077800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr14:78070600-78078200	Weak transcription	NH-A	brain
24	chr14:78070600-78078200	Weak transcription	Osteobl	bone
25	chr14:78070600-78078400	Weak transcription	NHDF-Ad	bronchial
26	chr14:78070600-78081400	Weak transcription	Ovary	ovary
27	chr14:78070600-78081600	Weak transcription	Esophagus	oesophagus
28	chr14:78070800-78075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr14:78070800-78076800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr14:78071200-78075600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr14:78071200-78075600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr14:78071400-78076800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr14:78071600-78076200	Enhancers	Primary B cells from peripheral blood	blood
34	chr14:78072200-78078200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr14:78072200-78078400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr14:78072400-78077800	Weak transcription	A549	lung
37	chr14:78072400-78081200	Weak transcription	Fetal Heart	heart
38	chr14:78072400-78081600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:78072600-78078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr14:78072800-78078200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:78072800-78078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr14:78072800-78081400	Weak transcription	Colonic Mucosa	Colon
43	chr14:78073000-78077200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr14:78073000-78078400	Weak transcription	HepG2	liver
45	chr14:78073400-78078400	Weak transcription	Small Intestine	intestine
46	chr14:78073400-78081600	Weak transcription	Psoas Muscle	Psoas
47	chr14:78073600-78075200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr14:78073600-78075600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr14:78073600-78076000	Enhancers	Brain Substantia Nigra	brain
50	chr14:78074000-78075000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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