Variant report

Variant	rs9421246
Chromosome Location	chr10:118608102-118608103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:118607451-118609603	GM12878	blood:	n/a	n/a
2	SPI1	chr10:118607676-118608290	HL-60	blood:	n/a	chr10:118608114-118608121
3	NR3C1	chr10:118607944-118608299	A549	lung:	n/a	chr10:118608073-118608099 chr10:118608078-118608093 chr10:118608079-118608093 chr10:118608073-118608099 chr10:118608138-118608153 chr10:118608073-118608099 chr10:118608078-118608094 chr10:118608073-118608099 chr10:118608073-118608099
4	NR3C1	chr10:118607981-118608198	A549	lung:	n/a	chr10:118608073-118608099 chr10:118608078-118608093 chr10:118608079-118608093 chr10:118608073-118608099 chr10:118608138-118608153 chr10:118608073-118608099 chr10:118608078-118608094 chr10:118608073-118608099 chr10:118608073-118608099
5	SPI1	chr10:118607756-118608168	HL-60	blood:	n/a	chr10:118608114-118608121
6	POLR2A	chr10:118607937-118609565	HCT-116	colon:	n/a	n/a
7	ZEB1	chr10:118607964-118608345	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:118607410-118609749	GM19193	blood:	n/a	n/a
9	MXI1	chr10:118607582-118608232	GM12878	blood:	n/a	n/a
10	RUNX3	chr10:118607412-118608614	GM12878	blood:	n/a	n/a
11	SIN3A	chr10:118607972-118608145	GM12878	blood:	n/a	n/a
12	RELA	chr10:118607352-118608230	GM10847	blood:	n/a	n/a
13	SPI1	chr10:118607418-118608345	GM12878	blood:	n/a	chr10:118608114-118608121
14	USF2	chr10:118608023-118608232	GM12878	blood:	n/a	n/a
15	SPI1	chr10:118607432-118608243	GM12891	blood:	n/a	chr10:118608114-118608121
16	NR3C1	chr10:118607958-118608272	A549	lung:	n/a	chr10:118608073-118608099 chr10:118608078-118608093 chr10:118608079-118608093 chr10:118608073-118608099 chr10:118608138-118608153 chr10:118608073-118608099 chr10:118608078-118608094 chr10:118608073-118608099 chr10:118608073-118608099
17	POLR2A	chr10:118607616-118608282	GM12891	blood:	n/a	n/a
18	POLR2A	chr10:118606833-118609969	GM12891	blood:	n/a	n/a
19	RELA	chr10:118607191-118608546	GM19193	blood:	n/a	n/a
20	RELA	chr10:118607209-118608425	GM12891	blood:	n/a	n/a
21	POLR2A	chr10:118607904-118609799	MCF10A-Er-Src	breast:	n/a	n/a
22	SPI1	chr10:118607427-118608294	GM12891	blood:	n/a	chr10:118608114-118608121
23	SPI1	chr10:118607717-118608130	GM12878	blood:	n/a	chr10:118608114-118608121
24	RELA	chr10:118607421-118608239	GM15510	blood:	n/a	n/a
25	WRNIP1	chr10:118607198-118608425	GM12878	blood:	n/a	n/a
26	POLR2A	chr10:118607986-118608259	GM12891	blood:	n/a	n/a
27	RELA	chr10:118607280-118609211	GM18951	blood:	n/a	n/a
28	RCOR1	chr10:118607537-118608102	GM12878	blood:	n/a	n/a
29	POLR2A	chr10:118607405-118609690	GM18505	blood:	n/a	n/a
30	RELA	chr10:118607490-118608116	GM12878	blood:	n/a	n/a
31	POLR2A	chr10:118607272-118609687	Raji	blood:	n/a	n/a
32	POLR2A	chr10:118607498-118609900	GM19099	blood:	n/a	n/a
33	RELA	chr10:118607472-118608890	GM19099	blood:	n/a	n/a
34	MTA3	chr10:118607330-118608413	GM12878	blood:	n/a	n/a
35	CHD2	chr10:118607545-118608125	GM12878	blood:	n/a	n/a
36	RELA	chr10:118607478-118608367	GM18505	blood:	n/a	n/a
37	TBP	chr10:118607585-118608265	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:118606549..118608975-chr10:118626771..118628550,2	MCF-7	breast:
2	chr10:118596184..118600317-chr10:118606262..118608808,4	MCF-7	breast:
3	chr10:118607956..118610219-chr10:118618457..118621328,3	MCF-7	breast:

Variant related genes	Relation type
ENO4	TF binding region
ENSG00000188316	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1023549	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs1023550	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1023551	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1023552	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1681752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170862	0.82[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4752015	0.85[ASN][1000 genomes]
rs7083543	0.86[ASN][1000 genomes]
rs7087685	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7896612	0.80[ASN][1000 genomes]
rs9420215	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs9421248	0.86[ASN][1000 genomes]
rs9421249	0.83[ASN][1000 genomes]
rs9421250	0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9421246	KIAA1598	cis	cerebellum	SCAN
rs9421246	KIAA1598	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:118598200-118608200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr10:118605600-118608400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:118606800-118608200	Enhancers	Primary B cells from peripheral blood	blood
4	chr10:118606800-118608200	Enhancers	Stomach Mucosa	stomach
5	chr10:118607200-118608200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:118607200-118608200	Enhancers	Fetal Intestine Small	intestine
7	chr10:118607200-118608400	Flanking Active TSS	GM12878-XiMat	blood
8	chr10:118607400-118608200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr10:118607400-118608200	Bivalent Enhancer	Fetal Thymus	thymus
10	chr10:118607400-118608600	Enhancers	Spleen	Spleen
11	chr10:118607400-118609400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:118607600-118608200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:118607600-118608200	Enhancers	Fetal Brain Female	brain
14	chr10:118607600-118608200	Enhancers	Fetal Stomach	stomach
15	chr10:118607600-118608400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:118607600-118609800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:118607800-118608200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:118607800-118608200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr10:118607800-118608200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr10:118607800-118608200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr10:118607800-118608200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr10:118607800-118608200	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr10:118607800-118608200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr10:118607800-118608200	Bivalent/Poised TSS	Thymus	Thymus
25	chr10:118607800-118608400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr10:118607800-118608400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr10:118607800-118608400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr10:118607800-118608400	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr10:118607800-118608400	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr10:118607800-118608400	Flanking Active TSS	HMEC	breast
31	chr10:118607800-118608400	Flanking Active TSS	NHEK	skin
32	chr10:118607800-118608600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr10:118607800-118608600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
34	chr10:118607800-118609600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr10:118607800-118609800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:118608000-118608200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr10:118608000-118608200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr10:118608000-118608200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:118608000-118608200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr10:118608000-118608200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:118608000-118608200	Bivalent Enhancer	Primary B cells from cord blood	blood
42	chr10:118608000-118608200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
43	chr10:118608000-118608200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:118608000-118608200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr10:118608000-118608200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:118608000-118608200	Active TSS	Brain Substantia Nigra	brain
47	chr10:118608000-118608200	Enhancers	Colonic Mucosa	Colon
48	chr10:118608000-118608200	Enhancers	Colon Smooth Muscle	Colon
49	chr10:118608000-118608200	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr10:118608000-118608200	Active TSS	Duodenum Smooth Muscle	Duodenum

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