Variant report

Variant	rs10168254
Chromosome Location	chr2:33823539-33823540
allele	A/C
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	MYC	chr2:33823405-33825273	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:33823416-33824811	GM12891	blood:	n/a	n/a
3	MYC	chr2:33823438-33825105	K562	blood:	n/a	n/a
4	POLR2A	chr2:33823494-33824891	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:33823532-33825015	Raji	blood:	n/a	n/a
6	POLR2A	chr2:33823514-33824920	GM19193	blood:	n/a	n/a
7	BATF	chr2:33823495-33823883	GM12878	blood:	n/a	n/a
8	ZNF143	chr2:33823474-33823674	GM12878	blood:	n/a	chr2:33823518-33823533
9	TBP	chr2:33823532-33823776	HepG2	liver:	n/a	n/a
10	MXI1	chr2:33823211-33825380	IMR90	lung:	n/a	n/a
11	WRNIP1	chr2:33823400-33824914	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:33823513-33824893	GM12878	blood:	n/a	n/a
13	MXI1	chr2:33822488-33825358	SK-N-SH	brain:	n/a	n/a
14	RELA	chr2:33823526-33824805	GM10847	blood:	n/a	n/a
15	POLR2A	chr2:33823321-33824979	GM12892	blood:	n/a	n/a
16	MAZ	chr2:33823441-33825073	IMR90	lung:	n/a	n/a
17	PML	chr2:33823245-33824969	GM12878	blood:	n/a	chr2:33823265-33823273
18	POLR2A	chr2:33823454-33824867	GM12878	blood:	n/a	n/a
19	MAX	chr2:33823459-33825185	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:33823457-33824888	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:33823501-33824853	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:33823511-33824978	IMR90	lung:	n/a	n/a
23	POLR2A	chr2:33823491-33824893	GM19099	blood:	n/a	n/a
24	POLR2A	chr2:33823435-33824882	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:33823330-33824946	GM12892	blood:	n/a	n/a
26	RELA	chr2:33823484-33824790	GM19193	blood:	n/a	n/a
27	PAX5	chr2:33823456-33824738	GM12878	blood:	n/a	chr2:33823973-33823990
28	MYC	chr2:33823501-33825042	K562	blood:	n/a	n/a
29	ZC3H11A	chr2:33823472-33823632	K562	blood:	n/a	n/a
30	POLR2A	chr2:33823286-33824872	GM12878	blood:	n/a	n/a
31	RUNX3	chr2:33823467-33824929	GM12878	blood:	n/a	n/a
32	RELA	chr2:33823536-33824844	GM18951	blood:	n/a	n/a
33	MAX	chr2:33823532-33825068	MCF-7	breast:	n/a	n/a
34	MAX	chr2:33823524-33825166	NB4	blood:	n/a	n/a
35	POLR2A	chr2:33823537-33824937	GM18526	blood:	n/a	n/a
36	POLR2A	chr2:33823405-33824675	GM12891	blood:	n/a	n/a
37	MAX	chr2:33823531-33825089	SK-N-SH	brain:	n/a	n/a
38	MAFK	chr2:33823485-33823829	HepG2	liver:	n/a	chr2:33823788-33823803
39	POLR2A	chr2:33823291-33824959	PBDE	blood:	n/a	n/a
40	HCFC1	chr2:33823253-33825166	Hela-S3	cervix:	n/a	n/a
41	SIN3AK20	chr2:33823342-33825194	MCF-7	breast:	n/a	n/a
42	RUNX3	chr2:33823405-33824984	GM12878	blood:	n/a	n/a
43	PML	chr2:33823525-33823920	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:33823410-33824919	GM18505	blood:	n/a	n/a
45	RFX5	chr2:33823417-33825030	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr2:33823453-33824693	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:33823509-33825019	HL-60	blood:	n/a	n/a
48	MAZ	chr2:33823512-33824911	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:33823373-33824712	GM12891	blood:	n/a	n/a
50	BCLAF1	chr2:33823407-33824716	GM12878	blood:	n/a	chr2:33824640-33824653 chr2:33824642-33824651

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33814233..33816944-chr2:33823198..33825061,2	K562	blood:
2	chr2:33813884..33820375-chr2:33821086..33825904,10	K562	blood:

Variant related genes	Relation type
ATP6V0E1P3	TF binding region
ENSG00000119812	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10173763	0.91[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10186755	0.82[EUR][1000 genomes]
rs10197783	0.92[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs11066	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1375198	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1375199	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs1448559	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2367811	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3023	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4494721	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4670217	0.81[ASN][1000 genomes]
rs6708570	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6718639	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6740336	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6757234	0.91[JPT][hapmap]
rs723241	0.91[JPT][hapmap]
rs723242	0.86[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10168254	FAM98A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33802200-33823600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33819000-33823600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33820400-33824800	Active TSS	GM12878-XiMat	blood
4	chr2:33821600-33823600	Enhancers	Spleen	Spleen
5	chr2:33821600-33825200	Active TSS	Ovary	ovary
6	chr2:33822000-33825400	Active TSS	NHLF	lung
7	chr2:33822200-33823600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:33822200-33823600	Enhancers	Small Intestine	intestine
9	chr2:33822200-33823600	Flanking Active TSS	HUVEC	blood vessel
10	chr2:33822200-33823800	Flanking Active TSS	Dnd41	blood
11	chr2:33822200-33826000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr2:33822400-33823800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:33822400-33824800	Active TSS	K562	blood
14	chr2:33822400-33825200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:33822400-33825400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:33822600-33823600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:33822600-33823600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr2:33822600-33823800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:33822600-33823800	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr2:33822600-33823800	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr2:33822600-33824000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr2:33822600-33825000	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr2:33822600-33825200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:33822600-33825200	Active TSS	Aorta	Aorta
25	chr2:33822600-33825200	Active TSS	Right Ventricle	heart
26	chr2:33822600-33825400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:33822600-33825400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr2:33822600-33825400	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr2:33822600-33825400	Active TSS	NH-A	brain
30	chr2:33822800-33823600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:33822800-33823600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:33822800-33823800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr2:33822800-33824200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:33822800-33824200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:33822800-33824200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr2:33822800-33825000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:33822800-33825200	Active TSS	H1 Cell Line	embryonic stem cell
38	chr2:33822800-33825200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:33822800-33825400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr2:33823000-33823600	Flanking Active TSS	Fetal Lung	lung
41	chr2:33823000-33824200	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr2:33823000-33824800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:33823000-33825000	Active TSS	NHEK	skin
44	chr2:33823000-33825200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:33823000-33825200	Active TSS	Psoas Muscle	Psoas
46	chr2:33823000-33825200	Active TSS	Right Atrium	heart
47	chr2:33823000-33825200	Active TSS	NHDF-Ad	bronchial
48	chr2:33823000-33825400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:33823000-33825400	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr2:33823000-33825400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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