Variant report

Variant	rs10739969
Chromosome Location	chr9:96866877-96866878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96864659..96867120-chr9:96928060..96930580,2	K562	blood:
2	chr9:96864692..96867836-chr9:96868310..96870488,3	K562	blood:
3	chr9:96866436..96868575-chr9:96873729..96876347,3	K562	blood:

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10117457	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10120093	0.86[AMR][1000 genomes]
rs10122334	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123954	0.94[ASN][1000 genomes]
rs10429556	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs10429603	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10435922	0.86[ASN][1000 genomes]
rs10435924	0.88[ASN][1000 genomes]
rs10739967	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10761308	0.82[ASN][1000 genomes]
rs10761309	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10761313	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10761315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821284	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10821285	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10821290	0.81[ASN][1000 genomes]
rs10993037	0.91[ASN][1000 genomes]
rs10993041	0.87[ASN][1000 genomes]
rs10993058	0.96[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs12351292	0.82[ASN][1000 genomes]
rs12684427	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs1316814	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1320547	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs1331216	0.82[ASN][1000 genomes]
rs1331217	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1331218	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1331219	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1343995	0.82[ASN][1000 genomes]
rs1360429	0.82[ASN][1000 genomes]
rs1411860	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1418251	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]
rs1576640	0.84[ASN][1000 genomes]
rs1590969	0.82[ASN][1000 genomes]
rs1592153	0.82[ASN][1000 genomes]
rs1832857	0.82[ASN][1000 genomes]
rs1854835	0.82[ASN][1000 genomes]
rs1933668	0.82[ASN][1000 genomes]
rs1933669	0.82[ASN][1000 genomes]
rs2026917	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2094927	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2150625	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.89[ASN][1000 genomes]
rs2153058	0.80[ASN][1000 genomes]
rs2153070	0.82[ASN][1000 genomes]
rs2153792	0.82[ASN][1000 genomes]
rs2211362	0.82[ASN][1000 genomes]
rs2225458	0.82[ASN][1000 genomes]
rs2226117	0.82[ASN][1000 genomes]
rs3763639	0.89[EUR][1000 genomes]
rs3847307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996241	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4282631	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4744308	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4744310	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744314	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479522	0.82[ASN][1000 genomes]
rs6479527	0.89[CEU][hapmap]
rs6479528	0.89[CEU][hapmap]
rs6479529	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7033481	0.82[ASN][1000 genomes]
rs7033898	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045643	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858069	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7867925	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs914295	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs914296	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs914297	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9299414	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs987511	0.82[ASN][1000 genomes]

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	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
5	nsv893591	chr9:96849137-96883271	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv2761543	chr9:96857735-96875582	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10739969	SPTLC1	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96824200-96869600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:96828200-96868200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:96829600-96872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:96845600-96885400	Weak transcription	Gastric	stomach
5	chr9:96846000-96870600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:96849000-96868800	Weak transcription	HepG2	liver
7	chr9:96849400-96869600	Weak transcription	HUVEC	blood vessel
8	chr9:96849400-96869800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:96849400-96883800	Weak transcription	Brain Germinal Matrix	brain
10	chr9:96849600-96870400	Weak transcription	Fetal Lung	lung
11	chr9:96850600-96870000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:96857200-96871000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:96857200-96882800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:96857400-96868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:96859200-96869600	Weak transcription	HSMMtube	muscle
16	chr9:96859200-96880800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:96860200-96870200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:96860200-96876200	Weak transcription	Esophagus	oesophagus
19	chr9:96860400-96867400	Weak transcription	Dnd41	blood
20	chr9:96860400-96873400	Weak transcription	NHLF	lung
21	chr9:96860600-96867000	Weak transcription	Psoas Muscle	Psoas
22	chr9:96860600-96870000	Weak transcription	A549	lung
23	chr9:96860600-96870600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:96860600-96870800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:96860600-96871000	Weak transcription	Brain Angular Gyrus	brain
26	chr9:96860600-96871000	Weak transcription	Right Ventricle	heart
27	chr9:96860600-96872800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:96860800-96868800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:96860800-96868800	Weak transcription	Fetal Brain Female	brain
30	chr9:96860800-96869600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:96860800-96870600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:96860800-96870800	Weak transcription	HSMM	muscle
33	chr9:96860800-96870800	Weak transcription	NH-A	brain
34	chr9:96860800-96870800	Weak transcription	NHDF-Ad	bronchial
35	chr9:96860800-96870800	Weak transcription	NHEK	skin
36	chr9:96860800-96871000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:96860800-96871000	Weak transcription	HMEC	breast
38	chr9:96860800-96872800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:96860800-96872800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:96860800-96886800	Weak transcription	Aorta	Aorta
41	chr9:96861000-96867000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:96861000-96869000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:96861000-96884000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:96861200-96870600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:96861200-96870600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:96861200-96871000	Weak transcription	Lung	lung
47	chr9:96861400-96871000	Weak transcription	Left Ventricle	heart
48	chr9:96861400-96875200	Weak transcription	Pancreas	Pancrea
49	chr9:96861400-96884600	Weak transcription	Ovary	ovary
50	chr9:96861600-96870800	Weak transcription	Fetal Muscle Trunk	muscle

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