Variant report

Variant	rs176906
Chromosome Location	chr14:78082110-78082111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:77782973..77788435-chr14:78081530..78084931,5	MCF-7	breast:
2	chr14:78069297..78071425-chr14:78081435..78083020,2	K562	blood:
3	chr14:77925306..77928562-chr14:78081993..78085089,3	MCF-7	breast:
4	chr14:78081876..78084095-chr14:78119324..78121053,2	MCF-7	breast:
5	chr14:78081719..78084170-chr17:57917300..57920054,2	MCF-7	breast:
6	chr14:78080102..78083060-chr14:78184904..78187965,3	K562	blood:
7	chr14:78064657..78067063-chr14:78079647..78083000,3	MCF-7	breast:
8	chr14:78068423..78071899-chr14:78079739..78082860,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000009830	Chromatin interaction
ENSG00000100577	Chromatin interaction
ENSG00000100591	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000258668	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12431525	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12431896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12433198	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12433737	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12433954	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12434701	0.87[ASN][1000 genomes]
rs12436803	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs176895	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176908	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176911	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176912	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751876	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17751917	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751923	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751980	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17751993	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17752165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17824984	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17825014	1.00[AFR][1000 genomes];0.94[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];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2364578	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886132	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35389286	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4497612	1.00[AFR][1000 genomes];0.94[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];0.91[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	0.94[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
rs176906	SPTLC2	cis	Nerve Tibial	GTEx
rs176906	ADCK1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78080200-78083800	Active TSS	GM12878-XiMat	blood
2	chr14:78081000-78082400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:78081200-78082200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:78081200-78082400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr14:78081200-78082400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr14:78081200-78082600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr14:78081200-78082800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr14:78081200-78083600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr14:78081400-78082200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr14:78081400-78082200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr14:78081400-78082200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr14:78081400-78082200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr14:78081400-78082200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr14:78081400-78082200	Flanking Active TSS	Fetal Brain Female	brain
15	chr14:78081400-78082200	Flanking Active TSS	Fetal Heart	heart
16	chr14:78081400-78082400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:78081400-78082400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr14:78081400-78082400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr14:78081400-78082400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr14:78081400-78082400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:78081400-78082400	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr14:78081400-78082400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr14:78081400-78082400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr14:78081400-78082400	Flanking Active TSS	Dnd41	blood
25	chr14:78081400-78082400	Flanking Active TSS	HUVEC	blood vessel
26	chr14:78081400-78082600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr14:78081400-78082600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr14:78081400-78082600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr14:78081400-78082600	Active TSS	Stomach Mucosa	stomach
30	chr14:78081400-78082600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr14:78081400-78083000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr14:78081400-78083000	Active TSS	K562	blood
33	chr14:78081400-78083200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:78081400-78083600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:78081400-78083600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr14:78081400-78083600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr14:78081400-78083600	Active TSS	Ovary	ovary
38	chr14:78081400-78083600	Active TSS	Right Atrium	heart
39	chr14:78081400-78083600	Active TSS	HSMMtube	muscle
40	chr14:78081400-78083600	Active TSS	NHLF	lung
41	chr14:78081400-78083800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr14:78081400-78083800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr14:78081400-78083800	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr14:78081600-78082200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr14:78081600-78082200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr14:78081600-78082200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr14:78081600-78082200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr14:78081600-78082200	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr14:78081600-78082200	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr14:78081600-78082200	Flanking Active TSS	Colon Smooth Muscle	Colon

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