Variant report

Variant	rs7029539
Chromosome Location	chr9:94864322-94864323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10512220	0.82[JPT][hapmap]
rs10739925	0.82[JPT][hapmap]
rs10761143	0.81[JPT][hapmap]
rs10820936	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10820938	0.82[MEX][hapmap]
rs10992221	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs10992234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1892268	0.82[JPT][hapmap]
rs1970121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297568	0.82[JPT][hapmap]
rs28727560	0.99[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2895201	0.82[JPT][hapmap]
rs3750440	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs3847308	0.89[JPT][hapmap]
rs4307406	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58129324	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6479400	0.82[JPT][hapmap]
rs6479403	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020136	0.82[JPT][hapmap]
rs7024583	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041193	0.82[JPT][hapmap]
rs7046540	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848874	0.82[JPT][hapmap]
rs7852067	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs7856177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7858659	0.81[CEU][hapmap];0.91[MEX][hapmap]
rs7860518	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7863564	0.84[EUR][1000 genomes]
rs7869504	0.82[JPT][hapmap]
rs7871444	0.82[JPT][hapmap]
rs7872515	1.00[CEU][hapmap];0.95[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][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	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
6	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7029539	SPTLC1	cis	parietal	SCAN
rs7029539	CDK20	cis	parietal	SCAN
rs7029539	FBP1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
2	chr9:94830800-94873800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:94840200-94865400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:94840600-94872000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:94842800-94866000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:94842800-94867600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:94842800-94876600	Weak transcription	Colonic Mucosa	Colon
8	chr9:94843000-94866000	Weak transcription	Lung	lung
9	chr9:94851400-94864400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:94851400-94865400	Weak transcription	Thymus	Thymus
11	chr9:94851400-94876600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:94851600-94865600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:94851800-94866000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:94851800-94867600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:94853200-94865400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr9:94857000-94875400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr9:94857200-94866200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr9:94857400-94865600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr9:94857800-94866200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:94858200-94867600	Weak transcription	Brain Angular Gyrus	brain
21	chr9:94858200-94869000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr9:94858200-94873600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr9:94858400-94865600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:94858400-94866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:94858400-94872200	Weak transcription	K562	blood
26	chr9:94858600-94865400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:94858600-94869400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr9:94858800-94873400	Weak transcription	GM12878-XiMat	blood
29	chr9:94859000-94870000	Weak transcription	HepG2	liver
30	chr9:94859200-94864400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:94859200-94864800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:94859200-94867600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr9:94859600-94872800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:94860400-94872000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:94860800-94864400	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:94860800-94865400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr9:94860800-94865600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr9:94860800-94865600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:94860800-94865600	Weak transcription	Aorta	Aorta
40	chr9:94860800-94865600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:94860800-94865600	Weak transcription	Fetal Stomach	stomach
42	chr9:94860800-94865600	Weak transcription	Left Ventricle	heart
43	chr9:94860800-94865600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:94860800-94865600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr9:94860800-94865600	Weak transcription	Right Ventricle	heart
46	chr9:94860800-94866000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:94860800-94872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:94860800-94873600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:94860800-94876000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:94860800-94876000	Weak transcription	Brain Substantia Nigra	brain

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