Variant report

Variant	rs1881385
Chromosome Location	chr9:94596781-94596782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94584589..94586242-chr9:94594324..94596965,2	K562	blood:
2	chr9:94596679..94601637-chr9:94602257..94606458,6	K562	blood:
3	chr9:94588743..94592515-chr9:94595352..94598489,3	MCF-7	breast:
4	chr9:94596693..94598646-chr9:94599586..94601943,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10761132	0.80[AMR][1000 genomes]
rs10761135	0.82[JPT][hapmap]
rs10820905	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10820906	0.91[CEU][hapmap]
rs10820910	0.82[JPT][hapmap]
rs10992123	0.92[CEU][hapmap]
rs10992124	0.87[CEU][hapmap]
rs10992126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992128	0.88[CEU][hapmap]
rs10992129	0.81[CEU][hapmap]
rs10992130	0.83[CEU][hapmap]
rs10992131	0.87[CEU][hapmap];0.80[AMR][1000 genomes]
rs10992134	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992135	0.83[CEU][hapmap]
rs10992136	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10992142	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs10992143	0.83[CEU][hapmap]
rs10992144	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992145	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11789730	0.92[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]
rs11790144	0.87[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs11791450	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376130	0.83[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs12376231	0.81[EUR][1000 genomes]
rs12376539	0.82[CEU][hapmap]
rs12378938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12551140	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12552292	0.85[CEU][hapmap]
rs12552858	0.85[CEU][hapmap]
rs12684524	0.83[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12684533	0.80[AMR][1000 genomes]
rs1528363	0.83[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1528364	0.83[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1534530	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534533	0.86[JPT][hapmap]
rs16907887	0.88[CEU][hapmap]
rs1881387	0.83[CEU][hapmap]
rs1997286	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2312732	0.92[CEU][hapmap]
rs2312733	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312734	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2312735	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4322068	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs4639579	0.88[CEU][hapmap]
rs4743857	0.91[CEU][hapmap];0.80[AMR][1000 genomes]
rs4744107	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4744111	0.86[JPT][hapmap]
rs55956910	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62563412	0.84[EUR][1000 genomes]
rs62564595	0.80[AMR][1000 genomes]
rs62564598	0.80[AMR][1000 genomes]
rs62565675	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6479374	0.92[CEU][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs6479375	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs6479376	0.88[CEU][hapmap]
rs7029950	0.92[CEU][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs7030661	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7031562	0.83[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes]
rs7033819	0.83[CEU][hapmap]
rs7045226	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7048756	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs7847473	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7850118	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7855417	0.88[CEU][hapmap]
rs7856144	0.92[CEU][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs7859331	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs7863061	0.87[CEU][hapmap]
rs7864311	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7865855	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867707	0.88[CEU][hapmap]
rs7870049	0.90[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap]
rs7874148	0.92[CEU][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv518372	chr9:94558126-94605908	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv6614	chr9:94571349-94610085	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1881385	SPTLC1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94594600-94610800	Enhancers	Fetal Thymus	thymus
2	chr9:94595400-94599800	Enhancers	Ovary	ovary
3	chr9:94595600-94597200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:94595600-94597400	Enhancers	Placenta	Placenta
5	chr9:94595600-94597600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94595600-94598200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:94595600-94598400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:94595600-94599200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:94595600-94599800	Weak transcription	K562	blood
10	chr9:94595600-94600000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr9:94595600-94600600	Enhancers	Fetal Stomach	stomach
12	chr9:94595800-94596800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:94595800-94596800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr9:94595800-94598400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:94595800-94598400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr9:94595800-94600200	Enhancers	Fetal Lung	lung
17	chr9:94596000-94596800	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr9:94596000-94598000	Enhancers	Fetal Intestine Small	intestine
19	chr9:94596000-94598200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:94596200-94597000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:94596200-94597000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:94596200-94597600	Enhancers	Fetal Intestine Large	intestine
23	chr9:94596200-94597800	Weak transcription	Right Atrium	heart
24	chr9:94596200-94598000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:94596200-94598200	Enhancers	Fetal Kidney	kidney
26	chr9:94596200-94598800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr9:94596200-94599000	Weak transcription	Gastric	stomach
28	chr9:94596400-94596800	Enhancers	Esophagus	oesophagus
29	chr9:94596400-94597200	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr9:94596400-94597600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:94596400-94605200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:94596600-94597000	Flanking Active TSS	Fetal Heart	heart
33	chr9:94596600-94597600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:94596600-94597600	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:94596600-94597800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:94596600-94598200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:94596600-94600200	Enhancers	Rectal Smooth Muscle	rectum
38	chr9:94596600-94600400	Weak transcription	NHDF-Ad	bronchial
39	chr9:94596600-94600600	Weak transcription	Spleen	Spleen

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