Variant report

Variant	rs12683797
Chromosome Location	chr9:94649104-94649105
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	chr9:94646595..94649139-chr9:94708273..94710120,2	K562	blood:
2	chr9:94647061..94649202-chr9:94659654..94661828,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10761133	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs10761134	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10761135	0.92[CEU][hapmap]
rs10820908	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10820910	0.84[CEU][hapmap]
rs10820914	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992124	0.80[CHB][hapmap]
rs10992128	0.80[CHB][hapmap]
rs10992129	0.80[CHB][hapmap]
rs10992130	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10992132	0.83[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10992137	0.83[CEU][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992139	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992140	0.82[EUR][1000 genomes]
rs10992143	0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs10992149	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992151	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992158	0.84[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs10992161	0.86[TSI][hapmap]
rs11789973	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12552858	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12555334	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs1534531	0.81[EUR][1000 genomes]
rs1534533	0.84[CEU][hapmap]
rs16907887	0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1881387	0.86[CHB][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1881392	0.83[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1892263	0.86[TSI][hapmap]
rs2030991	0.81[EUR][1000 genomes]
rs2030992	0.82[AMR][1000 genomes]
rs2141368	0.80[TSI][hapmap]
rs3905385	0.83[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs4347044	0.83[AMR][1000 genomes]
rs4430151	0.88[CEU][hapmap]
rs4517189	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4639579	0.80[CHB][hapmap];0.84[TSI][hapmap]
rs4744108	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744109	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744110	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744111	0.84[CEU][hapmap]
rs4744112	0.92[CEU][hapmap]
rs4744113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864279	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56088447	0.82[EUR][1000 genomes]
rs56308784	0.81[EUR][1000 genomes]
rs57688942	0.84[AMR][1000 genomes]
rs58202197	0.81[EUR][1000 genomes]
rs58431919	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59723153	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62564597	0.82[EUR][1000 genomes]
rs62564599	0.82[EUR][1000 genomes]
rs62565674	0.84[EUR][1000 genomes]
rs62565678	0.85[AMR][1000 genomes]
rs6479376	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs6479379	0.81[EUR][1000 genomes]
rs6479383	0.88[CEU][hapmap]
rs67944481	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7033819	0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs7039406	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs72746246	0.84[AMR][1000 genomes]
rs7850636	0.80[EUR][1000 genomes]
rs7855417	0.80[CHB][hapmap];0.84[TSI][hapmap]
rs7863061	0.80[CHB][hapmap]
rs7867567	0.81[EUR][1000 genomes]
rs7867707	0.80[CHB][hapmap];0.84[TSI][hapmap]
rs7870049	0.80[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12683797	SPTLC1	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94627000-94650800	Weak transcription	Gastric	stomach
2	chr9:94643200-94650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:94644400-94650800	Weak transcription	Right Atrium	heart
4	chr9:94646000-94649800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:94646000-94651600	Enhancers	K562	blood
6	chr9:94646000-94652600	Enhancers	Ovary	ovary
7	chr9:94646000-94654800	Enhancers	Fetal Lung	lung
8	chr9:94646200-94650800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:94646600-94651000	Enhancers	Placenta	Placenta
10	chr9:94646600-94654600	Enhancers	Fetal Stomach	stomach
11	chr9:94646600-94658200	Weak transcription	Fetal Heart	heart
12	chr9:94647200-94650000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:94647200-94650000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:94647200-94652600	Enhancers	Fetal Intestine Large	intestine
15	chr9:94647400-94649200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:94647600-94649400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr9:94647600-94650000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:94647800-94649800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:94647800-94652200	Weak transcription	Brain Substantia Nigra	brain
20	chr9:94648000-94649200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:94648000-94649200	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:94648000-94650800	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:94648400-94649200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr9:94648400-94651000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:94648600-94649200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr9:94648600-94649200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr9:94648600-94649400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr9:94648600-94649400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
29	chr9:94648600-94650000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:94648600-94650000	Enhancers	Fetal Kidney	kidney
31	chr9:94648600-94650000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr9:94648600-94650000	Enhancers	NH-A	brain
33	chr9:94648800-94649200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:94648800-94649400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr9:94648800-94649400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:94648800-94649400	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr9:94648800-94649600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr9:94648800-94653200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:94648800-94658400	Weak transcription	Pancreas	Pancrea
40	chr9:94648800-94661000	Weak transcription	Spleen	Spleen
41	chr9:94649000-94649200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr9:94649000-94649400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr9:94649000-94649400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:94649000-94649400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
45	chr9:94649000-94649400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:94649000-94649400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:94649000-94649600	Enhancers	Osteobl	bone
48	chr9:94649000-94649800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:94649000-94649800	Enhancers	NHLF	lung
50	chr9:94649000-94650000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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