Variant report

Variant	rs2312735
Chromosome Location	chr9:94605908-94605909
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	chr9:94596679..94601637-chr9:94602257..94606458,6	K562	blood:
2	chr9:94603914..94606181-chr9:94621038..94623335,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10761132	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10761135	0.82[JPT][hapmap]
rs10820905	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820906	0.91[CEU][hapmap]
rs10820910	0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992123	0.92[CEU][hapmap]
rs10992124	0.87[CEU][hapmap]
rs10992126	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10992145	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11789730	0.92[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes]
rs11790144	0.87[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs11791450	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12376130	0.83[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12376539	0.82[CEU][hapmap]
rs12378938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12551140	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.80[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];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12684533	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1528363	0.83[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1528364	0.83[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1534530	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534533	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16907887	0.88[CEU][hapmap]
rs1881385	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]
rs1881387	0.83[CEU][hapmap]
rs1997286	0.83[AMR][1000 genomes]
rs2312732	0.92[CEU][hapmap]
rs2312733	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2312734	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][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];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55956910	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563412	0.83[EUR][1000 genomes]
rs62564595	0.80[AMR][1000 genomes]
rs62564598	0.80[AMR][1000 genomes]
rs62565675	0.82[AMR][1000 genomes];0.81[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]
rs6479377	0.80[EUR][1000 genomes]
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];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7048756	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs7847473	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850118	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865855	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867707	0.88[CEU][hapmap]
rs7870049	0.90[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
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
rs2312735	SPTLC1	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94594600-94610800	Enhancers	Fetal Thymus	thymus
2	chr9:94601000-94606000	Weak transcription	Stomach Mucosa	stomach
3	chr9:94601800-94607400	Weak transcription	Gastric	stomach
4	chr9:94601800-94618400	Weak transcription	K562	blood
5	chr9:94602800-94611200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:94602800-94611600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:94603800-94607800	Enhancers	Ovary	ovary
8	chr9:94604000-94606200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr9:94604400-94606800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr9:94604600-94606000	Enhancers	Primary B cells from peripheral blood	blood
11	chr9:94604800-94606800	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:94604800-94607000	Enhancers	Thymus	Thymus
13	chr9:94604800-94607600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:94604800-94607800	Enhancers	Fetal Lung	lung
15	chr9:94604800-94610200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:94605000-94606200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:94605000-94606800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:94605000-94607000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr9:94605000-94607000	Enhancers	Brain Germinal Matrix	brain
20	chr9:94605000-94608400	Enhancers	Fetal Stomach	stomach
21	chr9:94605200-94606600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr9:94605200-94606800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:94605200-94607600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr9:94605200-94607600	Enhancers	Fetal Muscle Leg	muscle
25	chr9:94605400-94606000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr9:94605400-94606000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr9:94605400-94606200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:94605400-94606600	Enhancers	Primary B cells from cord blood	blood
29	chr9:94605400-94606800	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr9:94605400-94606800	Enhancers	Fetal Kidney	kidney
31	chr9:94605400-94607000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr9:94605400-94607400	Enhancers	NHLF	lung
33	chr9:94605400-94607600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr9:94605600-94606000	Enhancers	Brain Hippocampus Middle	brain
35	chr9:94605600-94606000	Weak transcription	Pancreas	Pancrea
36	chr9:94605600-94606000	Weak transcription	Right Atrium	heart
37	chr9:94605600-94606200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:94605600-94606200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:94605600-94606200	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr9:94605600-94606200	Enhancers	NHDF-Ad	bronchial
41	chr9:94605600-94606600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr9:94605600-94606600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:94605600-94606800	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr9:94605600-94606800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:94605600-94606800	Enhancers	Colonic Mucosa	Colon
46	chr9:94605600-94606800	Enhancers	Lung	lung
47	chr9:94605600-94607000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:94605600-94607000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr9:94605600-94607000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr9:94605600-94607000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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