Variant report

Variant	rs10992394
Chromosome Location	chr9:95433830-95433831
allele	A/G
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	MAX	chr9:95433449-95434152	HCT-116	colon:	n/a	n/a
2	MAX	chr9:95433434-95434073	SK-N-SH	brain:	n/a	n/a
3	EGR1	chr9:95433723-95434033	K562	blood:	n/a	n/a
4	RCOR1	chr9:95433353-95434184	IMR90	lung:	n/a	n/a
5	POLR2A	chr9:95433551-95434107	MCF-7	breast:	n/a	n/a
6	POLR2A	chr9:95431059-95434068	HUVEC	blood vessel:	n/a	n/a
7	YY1	chr9:95433429-95434022	SK-N-SH	brain:	n/a	chr9:95433793-95433803
8	FOS	chr9:95433645-95434014	HUVEC	blood vessel:	n/a	chr9:95433753-95433761 chr9:95433752-95433762 chr9:95433834-95433845
9	POLR2A	chr9:95433548-95434097	ECC-1	luminal epithelium:	n/a	n/a
10	MAX	chr9:95433670-95433940	Hela-S3	cervix:	n/a	n/a
11	MYC	chr9:95433547-95433939	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr9:95433643-95434012	MCF10A-Er-Src	breast:	n/a	chr9:95433753-95433761 chr9:95433752-95433762 chr9:95433834-95433845
13	POLR2A	chr9:95433482-95433896	Hela-S3	cervix:	n/a	n/a
14	FOS	chr9:95433606-95434003	MCF10A-Er-Src	breast:	n/a	chr9:95433753-95433761 chr9:95433752-95433762 chr9:95433834-95433845
15	POLR2A	chr9:95433384-95434157	SK-N-MC	brain:	n/a	n/a
16	YY1	chr9:95433591-95434046	HCT-116	colon:	n/a	chr9:95433793-95433803
17	TAF1	chr9:95433587-95434067	SK-N-SH	brain:	n/a	n/a
18	FOS	chr9:95433571-95434003	MCF10A-Er-Src	breast:	n/a	chr9:95433753-95433761 chr9:95433752-95433762 chr9:95433834-95433845
19	JUND	chr9:95433739-95433974	H1-hESC	embryonic stem cell:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
20	POLR2A	chr9:95433434-95433970	HepG2	liver:	n/a	n/a
21	FOSL2	chr9:95433658-95434029	HepG2	liver:	n/a	chr9:95433753-95433761 chr9:95433752-95433762
22	EGR1	chr9:95433508-95434167	HCT-116	colon:	n/a	n/a
23	JUND	chr9:95433744-95433892	H1-hESC	embryonic stem cell:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
24	MYC	chr9:95433523-95433953	MCF10A-Er-Src	breast:	n/a	n/a
25	SIN3AK20	chr9:95433572-95433964	SK-N-SH	brain:	n/a	n/a
26	YY1	chr9:95433531-95434009	SK-N-SH_RA	brain:	n/a	chr9:95433793-95433803
27	JUND	chr9:95433462-95434149	SK-N-SH	brain:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
28	STAT3	chr9:95433459-95434002	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr9:95430562-95434142	MCF10A-Er-Src	breast:	n/a	n/a
30	YY1	chr9:95433530-95434004	SK-N-SH_RA	brain:	n/a	chr9:95433793-95433803
31	YY1	chr9:95433397-95434160	SK-N-SH	brain:	n/a	chr9:95433793-95433803
32	POLR2A	chr9:95431202-95434109	HUVEC	blood vessel:	n/a	n/a
33	JUND	chr9:95433417-95434137	SK-N-SH	brain:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
34	POLR2A	chr9:95433672-95434150	ProgFib	skin:	n/a	n/a
35	JUND	chr9:95433690-95433985	HepG2	liver:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
36	JUND	chr9:95433360-95434289	SK-N-SH	brain:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
37	JUND	chr9:95433581-95433982	Hela-S3	cervix:	n/a	chr9:95433753-95433761 chr9:95433834-95433845 chr9:95433752-95433762
38	SP1	chr9:95433410-95434244	HCT-116	colon:	n/a	n/a
39	MAFF	chr9:95433563-95433850	K562	blood:	n/a	n/a
40	CBX3	chr9:95433404-95434172	K562	blood:	n/a	n/a
41	MYC	chr9:95433446-95433846	K562	blood:	n/a	n/a
42	NFIC	chr9:95433492-95434000	ECC-1	luminal epithelium:	n/a	n/a
43	STAT3	chr9:95433550-95433971	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr9:95433334-95434169	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr9:95433486-95434140	K562	blood:	n/a	n/a
46	GTF2F1	chr9:95433617-95433846	Hela-S3	cervix:	n/a	n/a
47	YY1	chr9:95433574-95434055	K562	blood:	n/a	chr9:95433793-95433803
48	SMC3	chr9:95433553-95433896	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr9:95433739-95434140	MCF-7	breast:	n/a	n/a
50	POLR2A	chr9:95433729-95434163	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95430814..95434525-chr9:95525652..95528883,5	K562	blood:
2	chr9:95088180..95090953-chr9:95432548..95434668,2	K562	blood:
3	chr9:95379288..95383213-chr9:95431051..95434876,7	MCF-7	breast:
4	chr9:95429562..95431238-chr9:95432570..95434492,2	K562	blood:
5	chr9:95087871..95089371-chr9:95431692..95434180,2	MCF-7	breast:
6	chr9:95085195..95087256-chr9:95431626..95434427,2	MCF-7	breast:
7	chr9:95432561..95435212-chr9:95564441..95567422,3	MCF-7	breast:
8	chr9:95432957..95435683-chr9:95486350..95488699,2	MCF-7	breast:
9	chr9:95395631..95397525-chr9:95432651..95435112,2	MCF-7	breast:
10	chr9:95382418..95385391-chr9:95432639..95435190,2	K562	blood:
11	chr9:95432638..95434160-chr9:95524447..95527402,2	MCF-7	breast:
12	chr9:95431331..95434473-chr9:95569877..95572688,3	MCF-7	breast:
13	chr9:95432219..95434684-chr9:95525652..95527897,3	K562	blood:

Variant related genes	Relation type
IPPK	TF binding region
ENSG00000127080	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000187984	Chromatin interaction
ENSG00000185963	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10820998	0.93[ASN][1000 genomes]
rs10821000	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10821001	0.84[ASN][1000 genomes]
rs10821002	0.80[EUR][1000 genomes]
rs10821003	0.84[ASN][1000 genomes]
rs10821004	0.82[ASN][1000 genomes]
rs10821005	0.81[ASN][1000 genomes]
rs10821017	0.85[EUR][1000 genomes]
rs10992382	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992384	0.80[AFR][1000 genomes]
rs10992390	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10992392	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10992396	0.94[ASN][1000 genomes]
rs10992402	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10992403	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992404	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992406	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992407	0.93[ASN][1000 genomes]
rs10992408	0.92[ASN][1000 genomes]
rs10992409	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10992412	0.92[ASN][1000 genomes]
rs10992413	0.80[EUR][1000 genomes]
rs10992414	0.84[ASN][1000 genomes]
rs10992416	0.84[ASN][1000 genomes]
rs10992417	0.84[ASN][1000 genomes]
rs10992419	0.80[EUR][1000 genomes]
rs10992420	0.84[ASN][1000 genomes]
rs10992422	0.82[ASN][1000 genomes]
rs10992423	0.81[ASN][1000 genomes]
rs10992426	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10992433	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10992475	0.82[EUR][1000 genomes]
rs1117670	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11533010	0.82[ASN][1000 genomes]
rs12236013	0.93[ASN][1000 genomes]
rs12236788	0.92[EUR][1000 genomes]
rs12237216	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685256	0.80[EUR][1000 genomes]
rs12685358	0.82[ASN][1000 genomes]
rs12686780	0.80[AFR][1000 genomes]
rs12686781	0.80[AFR][1000 genomes]
rs1407944	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1575460	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17366488	0.95[ASN][1000 genomes]
rs1853427	0.82[EUR][1000 genomes]
rs1980705	0.81[AMR][1000 genomes]
rs2088055	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2181584	0.82[ASN][1000 genomes]
rs2277164	0.82[EUR][1000 genomes]
rs2277166	0.84[AMR][1000 genomes]
rs2281888	0.81[AMR][1000 genomes]
rs3739605	0.81[ASN][1000 genomes]
rs41266683	0.83[AMR][1000 genomes]
rs58045868	0.83[AMR][1000 genomes]
rs58952648	0.81[ASN][1000 genomes]
rs6479426	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66493272	0.81[EUR][1000 genomes]
rs67601697	0.94[ASN][1000 genomes]
rs72618187	0.82[EUR][1000 genomes]
rs754600	0.97[ASN][1000 genomes]
rs7850871	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7851947	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7853617	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7856147	0.92[ASN][1000 genomes]
rs7857105	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7857502	0.93[ASN][1000 genomes]
rs7863882	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7863890	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7864889	0.83[AMR][1000 genomes]
rs7875050	0.92[ASN][1000 genomes]
rs879812	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs912261	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9775970	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10992394	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs10992394	CENPP	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95431600-95434000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:95432200-95434000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:95432600-95434000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr9:95432800-95434000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr9:95432800-95434000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:95433000-95434000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr9:95433000-95434000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:95433200-95434000	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:95433200-95434000	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr9:95433200-95434000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr9:95433200-95434200	Enhancers	Spleen	Spleen
12	chr9:95433400-95434000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:95433400-95434000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:95433400-95434000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr9:95433400-95434000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:95433400-95434000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:95433400-95434000	Flanking Active TSS	Liver	Liver
18	chr9:95433400-95434000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:95433400-95434000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr9:95433400-95434000	Enhancers	Gastric	stomach
21	chr9:95433400-95434000	Enhancers	Pancreas	Pancrea
22	chr9:95433400-95434000	Enhancers	Right Ventricle	heart
23	chr9:95433400-95434000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr9:95433400-95434000	Flanking Active TSS	Dnd41	blood
25	chr9:95433400-95434000	Flanking Active TSS	Hela-S3	cervix
26	chr9:95433400-95434200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:95433400-95434200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr9:95433400-95434200	Enhancers	Placenta	Placenta
29	chr9:95433400-95434200	Enhancers	Lung	lung
30	chr9:95433400-95442800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:95433600-95434000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:95433600-95434000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr9:95433600-95434000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr9:95433600-95434000	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr9:95433600-95434000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:95433600-95434000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr9:95433600-95434000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:95433600-95434000	Enhancers	Brain Angular Gyrus	brain
39	chr9:95433600-95434000	Enhancers	Colon Smooth Muscle	Colon
40	chr9:95433600-95434000	Enhancers	Fetal Intestine Large	intestine
41	chr9:95433600-95434000	Enhancers	Fetal Muscle Trunk	muscle
42	chr9:95433600-95434000	Enhancers	Fetal Muscle Leg	muscle
43	chr9:95433600-95434000	Enhancers	Fetal Stomach	stomach
44	chr9:95433600-95434000	Enhancers	Fetal Thymus	thymus
45	chr9:95433600-95434000	Flanking Active TSS	A549	lung
46	chr9:95433600-95434000	Flanking Active TSS	GM12878-XiMat	blood
47	chr9:95433600-95434000	Flanking Active TSS	K562	blood
48	chr9:95433600-95434200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:95433600-95434200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr9:95433600-95434200	Enhancers	Right Atrium	heart

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