Variant report

Variant	rs12235310
Chromosome Location	chr9:94829654-94829655
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	chr9:94828730..94831547-chr9:94834645..94837626,3	MCF-7	breast:
2	chr9:94828152..94830291-chr9:94832273..94834306,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10820926	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10820927	0.92[EUR][1000 genomes]
rs10820929	0.92[EUR][1000 genomes]
rs10820935	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820938	0.85[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10992173	0.84[EUR][1000 genomes]
rs10992176	0.84[EUR][1000 genomes]
rs10992177	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10992178	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10992179	0.92[EUR][1000 genomes]
rs10992180	0.92[EUR][1000 genomes]
rs10992183	0.92[EUR][1000 genomes]
rs10992190	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992215	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992216	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992221	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10992222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992231	0.81[ASN][1000 genomes]
rs10992233	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992235	0.88[EUR][1000 genomes]
rs10992236	0.88[EUR][1000 genomes]
rs11533009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12235309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12235495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236121	0.92[EUR][1000 genomes]
rs12237221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12237598	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12238682	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12337180	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12683519	0.81[EUR][1000 genomes]
rs16907979	1.00[CEU][hapmap]
rs16908003	0.84[EUR][1000 genomes]
rs16908021	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs16908135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1892267	0.84[EUR][1000 genomes]
rs1892269	0.84[EUR][1000 genomes]
rs2096388	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3858090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641129	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5000044	0.80[EUR][1000 genomes]
rs58909848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59114373	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59183854	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59232045	0.80[EUR][1000 genomes]
rs59856128	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022553	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7033030	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7042585	1.00[CEU][hapmap]
rs7847966	0.82[ASN][1000 genomes]
rs7849220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7852067	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7858659	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs7862826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872515	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.84[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	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
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	esv3324084	chr9:94821393-94830399	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
7	esv3482528	chr9:94821472-94830365	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	esv3482529	chr9:94821472-94830365	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12235310	SPTLC1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94810800-94860200	Weak transcription	Right Ventricle	heart
2	chr9:94812200-94832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:94817800-94877000	Weak transcription	Fetal Heart	heart
4	chr9:94820600-94844400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:94821400-94829800	Weak transcription	HMEC	breast
6	chr9:94822200-94832600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:94822400-94860200	Weak transcription	Stomach Mucosa	stomach
8	chr9:94823200-94842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:94823200-94844400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr9:94823400-94831000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:94823400-94832800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr9:94824000-94843600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr9:94824000-94844000	Strong transcription	Primary B cells from cord blood	blood
14	chr9:94824000-94860400	Weak transcription	Psoas Muscle	Psoas
15	chr9:94824400-94832800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:94824800-94844200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:94825000-94830000	Strong transcription	NHEK	skin
18	chr9:94825000-94833200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:94825200-94830000	Strong transcription	Brain Hippocampus Middle	brain
20	chr9:94825200-94833000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr9:94825200-94833000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr9:94825400-94830400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:94825400-94830400	Strong transcription	Colonic Mucosa	Colon
24	chr9:94825400-94844200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr9:94825600-94830200	Strong transcription	Fetal Lung	lung
26	chr9:94825600-94830800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:94825600-94833200	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr9:94825600-94834600	Strong transcription	Dnd41	blood
29	chr9:94825600-94844200	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr9:94825600-94844400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr9:94825800-94832600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:94826000-94830400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr9:94826000-94831000	Strong transcription	Fetal Brain Female	brain
34	chr9:94826000-94835000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:94826200-94830200	Strong transcription	Fetal Thymus	thymus
36	chr9:94826200-94830800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr9:94826200-94832800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:94826200-94833000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr9:94826200-94833200	Strong transcription	Fetal Intestine Large	intestine
40	chr9:94826200-94835000	Strong transcription	Adipose Nuclei	Adipose
41	chr9:94826400-94830200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr9:94826400-94830400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:94826400-94830400	Strong transcription	Brain Cingulate Gyrus	brain
44	chr9:94826400-94830400	Strong transcription	Brain Germinal Matrix	brain
45	chr9:94826400-94832600	Strong transcription	NHDF-Ad	bronchial
46	chr9:94826400-94835600	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:94826400-94843000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr9:94826600-94830400	Strong transcription	HepG2	liver
49	chr9:94826600-94833200	Strong transcription	Placenta	Placenta
50	chr9:94826600-94843800	Strong transcription	Duodenum Mucosa	Duodenum

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