Variant report

Variant	rs3858090
Chromosome Location	chr9:94853008-94853009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94851804..94854072-chr9:94856117..94858610,3	MCF-7	breast:
2	chr9:94849623..94853423-chr9:94859037..94861746,3	MCF-7	breast:
3	chr9:94850893..94855871-chr9:94857090..94860833,5	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10820926	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10820927	0.84[EUR][1000 genomes]
rs10820929	0.84[EUR][1000 genomes]
rs10820935	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10820938	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10992177	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs10992178	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs10992179	0.84[EUR][1000 genomes]
rs10992180	0.84[EUR][1000 genomes]
rs10992183	0.84[EUR][1000 genomes]
rs10992190	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992215	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992216	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992220	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992221	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10992222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992231	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10992233	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992235	0.81[EUR][1000 genomes]
rs10992236	0.81[EUR][1000 genomes]
rs11533009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12235309	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12235310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12235495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12236121	0.84[EUR][1000 genomes]
rs12237221	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12237598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238682	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12337180	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs16907979	1.00[CEU][hapmap]
rs16908021	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs16908135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16908137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2096388	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4641129	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58909848	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59114373	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59183854	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59856128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7022553	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7033030	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7042585	1.00[CEU][hapmap]
rs7847966	0.81[ASN][1000 genomes]
rs7849220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7852067	0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7858659	0.88[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7862826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7872515	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.83[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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3858090	SPTLC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
2	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
3	chr9:94822400-94860200	Weak transcription	Stomach Mucosa	stomach
4	chr9:94824000-94860400	Weak transcription	Psoas Muscle	Psoas
5	chr9:94827200-94856800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:94829000-94862600	Weak transcription	Hela-S3	cervix
7	chr9:94830000-94856800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:94830200-94856200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:94830200-94857000	Weak transcription	HUVEC	blood vessel
10	chr9:94830200-94860400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:94830800-94873800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:94833000-94857000	Weak transcription	Brain Anterior Caudate	brain
13	chr9:94833000-94858000	Weak transcription	Brain Angular Gyrus	brain
14	chr9:94839400-94861000	Weak transcription	HMEC	breast
15	chr9:94840200-94865400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:94840600-94872000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:94842200-94856400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:94842200-94860400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:94842200-94860400	Weak transcription	Pancreas	Pancrea
20	chr9:94842200-94860600	Weak transcription	Aorta	Aorta
21	chr9:94842200-94862400	Weak transcription	Esophagus	oesophagus
22	chr9:94842400-94860400	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:94842400-94861000	Weak transcription	Small Intestine	intestine
24	chr9:94842800-94860200	Weak transcription	Brain Germinal Matrix	brain
25	chr9:94842800-94866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:94842800-94867600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
28	chr9:94843000-94866000	Weak transcription	Lung	lung
29	chr9:94843400-94857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:94843400-94860200	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:94843400-94860400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:94843800-94856000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:94844000-94856600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr9:94844000-94856800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:94844000-94860600	Weak transcription	Spleen	Spleen
36	chr9:94844000-94861000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:94844200-94860200	Weak transcription	NHEK	skin
38	chr9:94849600-94853200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:94850200-94853200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:94850200-94853800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:94850400-94853400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:94850400-94860000	Weak transcription	Fetal Brain Female	brain
43	chr9:94850800-94853600	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr9:94850800-94857000	Weak transcription	Left Ventricle	heart
45	chr9:94850800-94860400	Weak transcription	Ovary	ovary
46	chr9:94851000-94857200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr9:94851000-94858000	Weak transcription	Adipose Nuclei	Adipose
48	chr9:94851200-94858000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:94851200-94859800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:94851200-94860000	Weak transcription	Rectal Mucosa Donor 31	rectum

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