Variant report

Variant	rs7045708
Chromosome Location	chr9:94621395-94621396
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94615667..94617326-chr9:94618676..94621395,2	K562	blood:
2	chr9:94619022..94622671-chr9:94625624..94629747,5	K562	blood:
3	chr9:94621154..94622760-chr9:94625624..94628222,3	K562	blood:
4	chr9:94620628..94622130-chr9:130690282..130691903,2	MCF-7	breast:
5	chr9:94603914..94606181-chr9:94621038..94623335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167103	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10118409	1.00[CEU][hapmap]
rs10121694	1.00[CEU][hapmap]
rs10122415	1.00[CEU][hapmap]
rs10512218	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11999739	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12002460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002884	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003273	0.84[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12003585	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16907830	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16907873	0.86[YRI][hapmap]
rs16907877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907940	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16908113	1.00[CEU][hapmap]
rs1881386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919104	1.00[CEU][hapmap]
rs28802998	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344138	1.00[CEU][hapmap]
rs4498616	1.00[CEU][hapmap]
rs4560856	1.00[CEU][hapmap]
rs4604504	1.00[CEU][hapmap]
rs56225147	0.97[ASN][1000 genomes]
rs59004196	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61160043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022887	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7031514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033888	1.00[CEU][hapmap]
rs7041908	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7045602	1.00[CEU][hapmap]
rs73519115	1.00[ASN][1000 genomes]
rs73519130	0.97[ASN][1000 genomes]
rs73519140	0.97[ASN][1000 genomes]
rs73651562	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73651565	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73651566	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73651574	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651579	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651580	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651581	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651582	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651583	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651595	0.97[ASN][1000 genomes]
rs73651596	0.97[ASN][1000 genomes]
rs7848959	1.00[CEU][hapmap]
rs7866996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7045708	SPTLC1	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94616400-94621400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:94616800-94621400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:94617400-94621400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:94617600-94621400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:94617600-94621400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:94617800-94621400	Enhancers	Colon Smooth Muscle	Colon
7	chr9:94617800-94621400	Enhancers	Rectal Smooth Muscle	rectum
8	chr9:94618600-94621400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:94618800-94621400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:94618800-94621400	Enhancers	Fetal Lung	lung
11	chr9:94619000-94621400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr9:94619000-94621400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:94619000-94621400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:94619200-94621400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:94619200-94621400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr9:94619600-94621400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr9:94619600-94621400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr9:94619800-94621400	Enhancers	Placenta	Placenta
19	chr9:94620200-94621400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:94620200-94621400	Enhancers	K562	blood
21	chr9:94620400-94621400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:94620400-94621400	Enhancers	Esophagus	oesophagus
23	chr9:94620400-94621400	Enhancers	Gastric	stomach
24	chr9:94620400-94622200	Weak transcription	Fetal Intestine Small	intestine
25	chr9:94620800-94621400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:94620800-94626400	Weak transcription	Ovary	ovary
27	chr9:94621000-94621800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:94621000-94626400	Weak transcription	Fetal Heart	heart
29	chr9:94621000-94627400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:94621200-94621800	Weak transcription	Fetal Stomach	stomach
31	chr9:94621200-94626000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:94621200-94626600	Weak transcription	Fetal Thymus	thymus

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