Variant report

Variant	rs9470847
Chromosome Location	chr6:38238551-38238552
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38238497..38240023-chr6:38248972..38251308,2	K562	blood:
2	chr6:38230666..38232627-chr6:38236052..38240073,5	MCF-7	breast:
3	chr6:38236548..38239476-chr6:38249471..38251086,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1475761	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1931767	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs228181	0.96[CEU][hapmap]
rs228182	0.91[CEU][hapmap]
rs228184	0.87[CEU][hapmap]
rs228185	0.91[CEU][hapmap]
rs228187	0.91[CEU][hapmap]
rs4711527	0.92[YRI][hapmap]
rs4711529	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714136	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4714140	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs4714144	0.96[CEU][hapmap]
rs6905637	0.96[CEU][hapmap]
rs6922620	0.91[CEU][hapmap]
rs9349067	0.85[EUR][1000 genomes]
rs9380737	0.83[CEU][hapmap]
rs9462423	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9462424	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9462425	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470833	0.92[YRI][hapmap]
rs9470848	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470849	0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470851	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9470856	0.96[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9470847	SPTLC3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38208200-38255000	Weak transcription	Ovary	ovary
2	chr6:38220600-38241600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:38223600-38256000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:38224400-38239000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:38224400-38267600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:38224600-38255200	Weak transcription	Primary B cells from cord blood	blood
7	chr6:38224800-38256400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:38225000-38255800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:38225200-38238600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:38225800-38239200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:38226400-38258000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:38226600-38256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:38226600-38257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:38230200-38253400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:38230800-38241200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:38230800-38256000	Weak transcription	Right Atrium	heart
17	chr6:38230800-38257800	Weak transcription	Pancreas	Pancrea
18	chr6:38231000-38250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:38232800-38241200	Weak transcription	Small Intestine	intestine
20	chr6:38233800-38241800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:38234400-38241600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:38234600-38238600	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:38234600-38238600	Enhancers	Brain Hippocampus Middle	brain
24	chr6:38234600-38238600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:38234800-38238800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:38235800-38240000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr6:38235800-38241800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:38236000-38239600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr6:38236000-38239800	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr6:38236000-38241600	Enhancers	Brain Substantia Nigra	brain
31	chr6:38236000-38241600	Enhancers	NH-A	brain
32	chr6:38236000-38241800	Enhancers	HSMMtube	muscle
33	chr6:38236200-38238600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:38236200-38238600	Enhancers	Fetal Kidney	kidney
35	chr6:38236200-38239200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:38236200-38239400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:38236200-38239800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr6:38236200-38239800	Enhancers	Adipose Nuclei	Adipose
39	chr6:38236400-38239600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr6:38236600-38238800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr6:38236600-38239800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:38237000-38241200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:38237200-38238600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:38237200-38238600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:38237200-38238800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:38237200-38239200	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:38237200-38239200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:38237200-38239600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:38237200-38239800	Enhancers	Brain Anterior Caudate	brain
50	chr6:38237200-38240600	Enhancers	Muscle Satellite Cultured Cells	--

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