Variant report

Variant	rs9398202
Chromosome Location	chr6:109780192-109780193
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr6:109779966-109780417	GM12878	blood:	n/a	n/a
2	NFATC1	chr6:109779796-109780496	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:109779768-109780531	GM12878	blood:	n/a	n/a
4	NFATC1	chr6:109780024-109780539	GM12878	blood:	n/a	n/a
5	SPI1	chr6:109780023-109780501	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:109779819-109780806	PANC-1	pancreas:	n/a	n/a
7	TBL1XR1	chr6:109780029-109780502	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:109779975-109780545	HL-60	blood:	n/a	n/a
9	RELA	chr6:109780022-109780561	GM19099	blood:	n/a	n/a
10	TCF3	chr6:109779905-109780295	GM12878	blood:	n/a	n/a
11	YY1	chr6:109779854-109780308	GM12878	blood:	n/a	n/a
12	FOXM1	chr6:109779935-109780414	GM12878	blood:	n/a	n/a
13	MXI1	chr6:109779989-109780587	GM12878	blood:	n/a	n/a
14	MAX	chr6:109780088-109780464	NB4	blood:	n/a	n/a
15	CHD2	chr6:109779945-109780589	GM12878	blood:	n/a	n/a
16	ZNF143	chr6:109780122-109780502	GM12878	blood:	n/a	n/a
17	EBF1	chr6:109779939-109780424	GM12878	blood:	n/a	n/a
18	USF1	chr6:109780121-109780413	GM12878	blood:	n/a	n/a
19	SPI1	chr6:109779963-109780442	GM12878	blood:	n/a	n/a
20	EP300	chr6:109779974-109780571	GM12878	blood:	n/a	n/a
21	FOS	chr6:109780148-109780314	MCF10A-Er-Src	breast:	n/a	n/a
22	RUNX3	chr6:109779899-109780392	GM12878	blood:	n/a	n/a
23	RCOR1	chr6:109780039-109780549	GM12878	blood:	n/a	n/a
24	SMC3	chr6:109779929-109780296	GM12878	blood:	n/a	n/a
25	CREB1	chr6:109779829-109780471	GM12878	blood:	n/a	n/a
26	RELA	chr6:109779746-109780748	GM12891	blood:	n/a	n/a
27	SPI1	chr6:109779947-109780652	HL-60	blood:	n/a	n/a
28	TCF12	chr6:109779997-109780329	GM12878	blood:	n/a	n/a
29	EP300	chr6:109779994-109780374	GM12878	blood:	n/a	n/a
30	SPI1	chr6:109780066-109780561	HL-60	blood:	n/a	n/a
31	ATF2	chr6:109779889-109780652	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:109779984-109780451	HL-60	blood:	n/a	n/a
33	STAT3	chr6:109780117-109780484	GM12878	blood:	n/a	n/a
34	EP300	chr6:109779969-109780432	GM12878	blood:	n/a	n/a
35	RFX5	chr6:109780132-109780336	GM12878	blood:	n/a	n/a
36	MAZ	chr6:109780007-109780352	GM12878	blood:	n/a	n/a
37	USF2	chr6:109780080-109780481	GM12878	blood:	n/a	n/a
38	WRNIP1	chr6:109780103-109780794	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:109779918-109780843	GM12878	blood:	n/a	n/a
40	EBF1	chr6:109780075-109780540	GM12878	blood:	n/a	n/a
41	MTA3	chr6:109779687-109780759	GM12878	blood:	n/a	n/a
42	RELA	chr6:109779851-109780680	GM18951	blood:	n/a	n/a
43	NFIC	chr6:109779863-109780495	GM12878	blood:	n/a	n/a
44	MAX	chr6:109780035-109780418	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109779538..109782087-chr6:109794538..109796974,3	K562	blood:
2	chr6:109779059..109781769-chr6:109783298..109786186,2	MCF-7	breast:
3	chr6:109778593..109780391-chr6:109793154..109794770,2	K562	blood:
4	chr6:109704063..109706352-chr6:109779634..109782625,2	K562	blood:

No data

Variant related genes	Relation type
MICAL1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1046943	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10872033	0.80[EUR][1000 genomes]
rs12214147	0.80[EUR][1000 genomes]
rs12529733	0.85[CEU][hapmap]
rs1476387	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17070591	0.80[EUR][1000 genomes]
rs2236084	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2277113	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35146243	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35260632	0.81[AMR][1000 genomes]
rs3734652	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3778478	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3799842	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs4636056	0.80[EUR][1000 genomes]
rs4945831	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4946976	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6939548	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7751582	0.80[EUR][1000 genomes]
rs7753224	0.86[YRI][hapmap]
rs910730	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9372213	0.96[CEU][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs9386799	0.81[EUR][1000 genomes]
rs9480956	0.80[EUR][1000 genomes]
rs9480958	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9487103	0.80[EUR][1000 genomes]
rs9487128	0.86[YRI][hapmap]
rs9487173	0.87[YRI][hapmap]
rs9791241	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9398202	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs9398202	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs9398202	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs9398202	SMPD2	cis	Whole Blood	GTEx
rs9398202	MICAL1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109777600-109780600	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr6:109777600-109780600	Flanking Active TSS	GM12878-XiMat	blood
3	chr6:109777600-109780800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:109777600-109781000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr6:109777600-109781000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:109777600-109782000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:109777600-109783200	Weak transcription	Hela-S3	cervix
8	chr6:109777800-109780800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:109777800-109780800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr6:109777800-109781600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:109777800-109782400	Weak transcription	Dnd41	blood
12	chr6:109777800-109786800	Weak transcription	Gastric	stomach
13	chr6:109777800-109786800	Weak transcription	Ovary	ovary
14	chr6:109778000-109780400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:109778000-109780600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:109778000-109780600	Enhancers	K562	blood
17	chr6:109778000-109780800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:109778000-109781000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:109778000-109783000	Weak transcription	HMEC	breast
20	chr6:109778000-109783000	Weak transcription	Osteobl	bone
21	chr6:109778000-109783200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:109778000-109786800	Weak transcription	Pancreas	Pancrea
23	chr6:109778000-109786800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:109778200-109780200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:109778200-109780600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr6:109778200-109780600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:109778200-109780600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:109778200-109780800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr6:109778200-109781800	Enhancers	Primary B cells from cord blood	blood
30	chr6:109778200-109782000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:109778200-109782400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:109778200-109782400	Weak transcription	Fetal Kidney	kidney
33	chr6:109778200-109782600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:109778200-109783200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:109778200-109784200	Weak transcription	Fetal Stomach	stomach
36	chr6:109778200-109785000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:109778200-109785600	Weak transcription	Fetal Brain Female	brain
38	chr6:109778200-109786600	Weak transcription	Fetal Heart	heart
39	chr6:109778200-109786800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:109778200-109786800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:109778200-109786800	Weak transcription	Fetal Brain Male	brain
42	chr6:109778200-109787000	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:109778400-109780400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr6:109778400-109781200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:109778400-109781200	Enhancers	Stomach Mucosa	stomach
46	chr6:109778400-109782400	Weak transcription	HUVEC	blood vessel
47	chr6:109778400-109783000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:109778400-109783000	Weak transcription	HepG2	liver
49	chr6:109778400-109783200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:109778400-109786800	Weak transcription	Rectal Smooth Muscle	rectum

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