Variant report

Variant	rs12002478
Chromosome Location	chr9:94603970-94603971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94597586..94601465-chr9:94602257..94605897,5	K562	blood:
2	chr9:94602912..94604839-chr9:94617568..94620449,2	MCF-7	breast:
3	chr9:94602829..94605124-chr9:94607630..94609855,2	MCF-7	breast:
4	chr9:94596679..94601637-chr9:94602257..94606458,6	K562	blood:
5	chr9:94603914..94606181-chr9:94621038..94623335,2	MCF-7	breast:
6	chr9:94602829..94604983-chr9:94613867..94616038,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12002827	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12002851	0.82[ASW][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12004009	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]
rs16907873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032520	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]
rs73651567	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73651569	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651570	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847748	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7849644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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]
rs7866996	1.00[CEU][hapmap]
rs7874163	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][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
rs12002478	SPTLC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94594600-94610800	Enhancers	Fetal Thymus	thymus
2	chr9:94596400-94605200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:94597000-94605800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:94598000-94604800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:94598200-94605600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:94599200-94604400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:94599200-94604600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:94600000-94605600	Weak transcription	Colonic Mucosa	Colon
9	chr9:94601000-94604600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:94601000-94605000	Weak transcription	Spleen	Spleen
11	chr9:94601000-94605600	Weak transcription	Fetal Intestine Large	intestine
12	chr9:94601000-94605600	Weak transcription	Lung	lung
13	chr9:94601000-94606000	Weak transcription	Stomach Mucosa	stomach
14	chr9:94601200-94605000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:94601200-94605000	Weak transcription	Brain Germinal Matrix	brain
16	chr9:94601200-94605200	Weak transcription	Fetal Intestine Small	intestine
17	chr9:94601400-94605400	Weak transcription	NHLF	lung
18	chr9:94601400-94605600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:94601400-94605800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:94601400-94605800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:94601400-94605800	Weak transcription	Fetal Brain Female	brain
22	chr9:94601600-94605400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:94601600-94605800	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:94601800-94605400	Weak transcription	Pancreas	Pancrea
25	chr9:94601800-94607400	Weak transcription	Gastric	stomach
26	chr9:94601800-94618400	Weak transcription	K562	blood
27	chr9:94602000-94605400	Weak transcription	Fetal Kidney	kidney
28	chr9:94602400-94604200	Weak transcription	Fetal Lung	lung
29	chr9:94602400-94605400	Weak transcription	Right Atrium	heart
30	chr9:94602600-94604800	Weak transcription	Primary B cells from cord blood	blood
31	chr9:94602600-94605400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:94602800-94604600	Enhancers	Stomach Smooth Muscle	stomach
33	chr9:94602800-94611200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:94602800-94611600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:94603000-94604800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:94603000-94605000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:94603400-94605000	Weak transcription	Fetal Stomach	stomach
38	chr9:94603400-94605600	Enhancers	Colon Smooth Muscle	Colon
39	chr9:94603600-94604000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:94603600-94604000	Weak transcription	Fetal Heart	heart
41	chr9:94603600-94604800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr9:94603800-94604400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr9:94603800-94605200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:94603800-94605600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:94603800-94607800	Enhancers	Ovary	ovary

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