Variant report

Variant	rs16907887
Chromosome Location	chr9:94607294-94607295
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94600587..94602440-chr9:94606824..94609770,3	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10820906	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs10820907	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10820908	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10820914	0.81[AMR][1000 genomes]
rs10992123	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992124	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992128	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992129	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992131	0.92[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992132	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992134	0.84[CEU][hapmap]
rs10992135	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992136	0.84[CEU][hapmap]
rs10992137	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992139	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992140	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992142	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992143	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992144	0.88[CEU][hapmap]
rs10992145	0.84[CEU][hapmap]
rs10992149	0.81[EUR][1000 genomes]
rs10992151	0.81[AMR][1000 genomes]
rs11789730	0.88[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs11789973	0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs11790144	0.92[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs11791450	0.82[CEU][hapmap]
rs12376130	0.80[AMR][1000 genomes]
rs12376231	0.82[EUR][1000 genomes]
rs12376539	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs12378938	0.89[CEU][hapmap]
rs12551140	0.92[CEU][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs12552292	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12552858	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12555334	0.80[CEU][hapmap]
rs12683797	0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1534531	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534535	0.81[EUR][1000 genomes]
rs1881385	0.88[CEU][hapmap]
rs1881387	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1881392	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1997286	0.80[EUR][1000 genomes]
rs2141368	0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs2312732	0.88[CEU][hapmap]
rs2312734	0.92[CEU][hapmap];0.81[CHD][hapmap];0.80[MEX][hapmap];0.81[EUR][1000 genomes]
rs2312735	0.88[CEU][hapmap]
rs2841691	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4322068	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4517189	0.81[AMR][1000 genomes]
rs4639579	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743857	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4744107	0.88[CEU][hapmap]
rs4744108	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744109	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs4744110	0.94[GIH][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs4744113	0.81[EUR][1000 genomes]
rs55663665	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55864279	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56088447	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56308784	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58431919	0.81[AMR][1000 genomes]
rs59723153	0.81[AMR][1000 genomes]
rs62564595	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62564597	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62564598	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62564599	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62565674	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479374	0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes]
rs6479375	0.95[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6479376	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67944481	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7019210	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7029950	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs7030661	0.84[CEU][hapmap]
rs7031562	0.88[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7033819	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7039406	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7045226	0.84[CEU][hapmap]
rs7045333	0.83[EUR][1000 genomes]
rs7048756	0.87[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72746206	0.83[EUR][1000 genomes]
rs7850118	0.81[CEU][hapmap]
rs7850636	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7855417	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7856144	0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7859331	0.96[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7863061	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867707	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7870902	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7874148	0.96[CEU][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
rs16907887	SPTLC1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94594600-94610800	Enhancers	Fetal Thymus	thymus
2	chr9:94601800-94607400	Weak transcription	Gastric	stomach
3	chr9:94601800-94618400	Weak transcription	K562	blood
4	chr9:94602800-94611200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:94602800-94611600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94603800-94607800	Enhancers	Ovary	ovary
7	chr9:94604800-94607600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:94604800-94607800	Enhancers	Fetal Lung	lung
9	chr9:94604800-94610200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:94605000-94608400	Enhancers	Fetal Stomach	stomach
11	chr9:94605200-94607600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr9:94605200-94607600	Enhancers	Fetal Muscle Leg	muscle
13	chr9:94605400-94607400	Enhancers	NHLF	lung
14	chr9:94605400-94607600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr9:94605600-94609600	Weak transcription	Spleen	Spleen
16	chr9:94605800-94607600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:94605800-94607800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr9:94606400-94609000	Enhancers	Fetal Heart	heart
19	chr9:94606600-94607800	Enhancers	Colon Smooth Muscle	Colon
20	chr9:94606600-94609800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:94606600-94616600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:94606800-94607600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:94606800-94607600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:94606800-94607800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:94606800-94607800	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr9:94606800-94607800	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:94606800-94608000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:94606800-94608200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:94606800-94609200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:94606800-94609200	Weak transcription	Fetal Kidney	kidney
31	chr9:94606800-94609600	Weak transcription	Primary T cells from cord blood	blood
32	chr9:94606800-94609600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:94606800-94609800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:94606800-94609800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:94606800-94615000	Weak transcription	Right Atrium	heart
36	chr9:94606800-94619600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:94607000-94607400	Weak transcription	Fetal Intestine Small	intestine
38	chr9:94607000-94607400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:94607000-94607400	Enhancers	Stomach Smooth Muscle	stomach
40	chr9:94607000-94607600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:94607000-94608200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:94607000-94608400	Weak transcription	Placenta	Placenta
43	chr9:94607000-94609600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:94607000-94609600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:94607000-94609800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:94607000-94609800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:94607000-94609800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:94607000-94610200	Weak transcription	Fetal Brain Male	brain
49	chr9:94607200-94607400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr9:94607200-94608400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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