Variant report

Variant	rs1418251
Chromosome Location	chr9:96848077-96848078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96845151..96851769-chr9:96927067..96931565,10	K562	blood:
2	chr9:96847188..96849533-chr9:96856467..96859477,3	K562	blood:
3	chr9:96848027..96849533-chr9:96856014..96858976,2	K562	blood:
4	chr9:96792104..96794426-chr9:96846620..96848608,2	MCF-7	breast:
5	chr9:96845151..96850974-chr9:96927067..96931575,8	K562	blood:
6	chr9:96844456..96848566-chr9:96937566..96941042,3	K562	blood:
7	chr9:96847639..96850039-chr9:96863471..96865147,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199165	Chromatin interaction
ENSG00000269946	Chromatin interaction
ENSG00000269929	Chromatin interaction
ENSG00000158079	Chromatin interaction
ENSG00000199072	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10117457	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10120093	0.91[AMR][1000 genomes]
rs10122334	0.91[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10123954	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10429556	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10429603	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10435922	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10435924	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739967	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739969	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10761308	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761309	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761313	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10761315	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821284	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10821285	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10821290	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10993037	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993041	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993058	0.92[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs12351292	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12684427	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs1316814	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1320547	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs1331216	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331218	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1331219	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1343995	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1360429	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1411860	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1576640	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1590969	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1592153	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1832857	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1854835	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1933668	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1933669	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1933679	0.82[EUR][1000 genomes]
rs2026917	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2094927	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2150625	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2153058	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2153070	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2153792	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2211362	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2225458	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2226117	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35883789	0.85[EUR][1000 genomes]
rs3847307	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3996241	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4282631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4406469	0.81[EUR][1000 genomes]
rs4744308	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744310	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744314	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744316	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479522	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6479527	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs6479528	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs6479529	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7033481	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7033898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7045643	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7858069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7867925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914295	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs914296	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs914297	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9299414	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs987511	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
3	nsv1043704	chr9:96816552-96873018	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1418251	SPTLC1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96822400-96859800	Weak transcription	Psoas Muscle	Psoas
2	chr9:96824200-96860000	Weak transcription	Aorta	Aorta
3	chr9:96824200-96869600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:96824400-96850000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:96828200-96848400	Weak transcription	Fetal Intestine Large	intestine
6	chr9:96828200-96848600	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:96828200-96859600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:96828200-96860800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr9:96828200-96862000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:96828200-96868200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:96828400-96848400	Weak transcription	NHDF-Ad	bronchial
12	chr9:96828400-96848600	Weak transcription	A549	lung
13	chr9:96829600-96872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:96832000-96859800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:96834000-96848600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:96834400-96859800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:96835400-96861800	Weak transcription	Primary B cells from cord blood	blood
18	chr9:96837000-96857400	Weak transcription	HSMM	muscle
19	chr9:96837200-96848400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:96837200-96857400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:96837200-96858600	Weak transcription	Dnd41	blood
22	chr9:96837200-96859800	Weak transcription	Fetal Intestine Small	intestine
23	chr9:96837400-96848600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:96837400-96848600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:96837400-96850600	Weak transcription	Adipose Nuclei	Adipose
26	chr9:96837400-96860200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:96837600-96859200	Weak transcription	Primary T cells from cord blood	blood
28	chr9:96837800-96848600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:96840200-96863600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:96840400-96850000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:96842600-96858200	Weak transcription	HSMMtube	muscle
32	chr9:96843600-96857000	Weak transcription	Colonic Mucosa	Colon
33	chr9:96845000-96853400	Weak transcription	GM12878-XiMat	blood
34	chr9:96845200-96848600	Weak transcription	Stomach Mucosa	stomach
35	chr9:96845200-96857600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:96845600-96848200	Weak transcription	Fetal Heart	heart
37	chr9:96845600-96848600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:96845600-96848600	Weak transcription	Fetal Stomach	stomach
39	chr9:96845600-96848600	Weak transcription	NHLF	lung
40	chr9:96845600-96858200	Weak transcription	Right Ventricle	heart
41	chr9:96845600-96858400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr9:96845600-96885400	Weak transcription	Gastric	stomach
43	chr9:96845800-96848600	Active TSS	Brain Anterior Caudate	brain
44	chr9:96846000-96848400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:96846000-96848400	Weak transcription	Fetal Kidney	kidney
46	chr9:96846000-96848400	Weak transcription	Fetal Lung	lung
47	chr9:96846000-96870600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:96846200-96859800	Weak transcription	Ovary	ovary
49	chr9:96846800-96849400	Enhancers	NH-A	brain
50	chr9:96847000-96848600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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