Variant report

Variant	rs11159275
Chromosome Location	chr14:78018246-78018247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr14:78018100-78018330	HCPEpiC	choroid plexus:	n/a	n/a
2	CTCF	chr14:78018160-78018310	GM12872	blood:	n/a	n/a
3	CTCF	chr14:78018180-78018330	HPAF	blood vessel:	n/a	n/a
4	CTCF	chr14:78018160-78018310	AoAF	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78013266..78015094-chr14:78015615..78018423,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL587P	TF binding region
ENSG00000240233	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11159276	0.89[CHB][hapmap]
rs11621440	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12590866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17751727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003633	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272587	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2272588	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2284229	0.87[YRI][hapmap]
rs2886131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34153615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063635	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36111947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56202833	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56225479	0.94[ASN][1000 genomes]
rs60221235	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153686	0.89[ASN][1000 genomes]
rs7158568	0.81[CHB][hapmap]
rs741850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003812	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8014527	0.94[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
rs11159275	SPTLC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77970200-78047200	Weak transcription	Fetal Heart	heart
2	chr14:77978800-78042200	Weak transcription	Fetal Brain Male	brain
3	chr14:77987400-78021000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr14:77987800-78060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:77988400-78029400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr14:77997800-78018800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr14:78002200-78020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr14:78006800-78019000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr14:78008200-78019000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:78009600-78019400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr14:78009600-78021200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:78009600-78030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr14:78009800-78050800	Weak transcription	Psoas Muscle	Psoas
14	chr14:78010000-78018800	Strong transcription	NH-A	brain
15	chr14:78010000-78019800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:78010000-78029800	Strong transcription	Primary T cells from cord blood	blood
17	chr14:78010200-78019000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:78010200-78020400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr14:78010200-78026800	Weak transcription	Stomach Mucosa	stomach
20	chr14:78010400-78018600	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr14:78010400-78030000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:78010600-78019200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr14:78010600-78025000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:78010800-78018600	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr14:78010800-78019000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr14:78011000-78020000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr14:78011000-78031800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr14:78011200-78019000	Strong transcription	Osteobl	bone
29	chr14:78011200-78045800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:78011400-78019000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr14:78011400-78037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:78012800-78019000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr14:78013000-78018800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr14:78013200-78030600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr14:78013400-78025800	Strong transcription	HSMM	muscle
37	chr14:78013600-78018400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr14:78013600-78018800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr14:78013600-78026200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:78013800-78019200	Strong transcription	Fetal Stomach	stomach
41	chr14:78014000-78018800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr14:78014400-78018800	Strong transcription	Fetal Intestine Large	intestine
43	chr14:78014600-78018800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr14:78014600-78018800	Strong transcription	GM12878-XiMat	blood
45	chr14:78014600-78019400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr14:78015000-78018800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr14:78015200-78020400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr14:78015200-78023200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr14:78015200-78024400	Strong transcription	HUVEC	blood vessel
50	chr14:78015800-78020800	Weak transcription	Stomach Smooth Muscle	stomach

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