Variant report

Variant	rs16907940
Chromosome Location	chr9:94643616-94643617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94636703..94639887-chr9:94643001..94646217,3	K562	blood:
2	chr9:94488540..94490420-chr9:94643419..94645317,2	MCF-7	breast:
3	chr9:94633023..94637402-chr9:94642921..94647325,4	MCF-7	breast:
4	chr9:94643600..94645407-chr9:94647843..94650643,2	MCF-7	breast:
5	chr9:94643211..94646019-chr9:94657149..94659875,2	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10114686	1.00[CEU][hapmap]
rs10512218	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999739	1.00[JPT][hapmap]
rs12002460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12002884	0.97[ASN][1000 genomes]
rs12003273	0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12340061	1.00[CEU][hapmap]
rs16907877	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16907893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1881386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28802998	0.97[ASN][1000 genomes]
rs56225147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61160043	0.97[ASN][1000 genomes]
rs7031514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7035117	1.00[CEU][hapmap]
rs7041908	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs7045073	1.00[CEU][hapmap]
rs7045708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73519115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73519130	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73519140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651574	0.97[ASN][1000 genomes]
rs73651579	0.97[ASN][1000 genomes]
rs73651580	0.97[ASN][1000 genomes]
rs73651581	0.97[ASN][1000 genomes]
rs73651582	0.97[ASN][1000 genomes]
rs73651583	0.97[ASN][1000 genomes]
rs73651584	0.97[ASN][1000 genomes]
rs73651595	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73651596	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7863425	1.00[CEU][hapmap]
rs7866996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9969713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	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
4	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16907940	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL
rs16907940	SPTLC1	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94627000-94650800	Weak transcription	Gastric	stomach
2	chr9:94627200-94648600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:94627600-94647400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:94633000-94644600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:94636600-94646000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:94636600-94647200	Weak transcription	Fetal Intestine Large	intestine
7	chr9:94636800-94645400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:94637800-94645000	Weak transcription	Fetal Intestine Small	intestine
9	chr9:94638200-94646200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:94638400-94646000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:94638800-94644200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:94639200-94645200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:94639400-94645000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:94639800-94644000	Weak transcription	Right Atrium	heart
15	chr9:94639800-94647400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:94640400-94645200	Strong transcription	Fetal Stomach	stomach
17	chr9:94641600-94644400	Genic enhancers	K562	blood
18	chr9:94641800-94644800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:94642000-94643800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:94642600-94644400	Enhancers	Fetal Heart	heart
21	chr9:94642800-94646400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:94643000-94644200	Enhancers	Fetal Lung	lung
23	chr9:94643200-94643800	Weak transcription	Ovary	ovary
24	chr9:94643200-94644200	Weak transcription	Left Ventricle	heart
25	chr9:94643200-94646000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:94643200-94650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:94643400-94648600	Weak transcription	Pancreas	Pancrea
28	chr9:94643600-94646400	Weak transcription	Colon Smooth Muscle	Colon

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