Variant report

Variant	rs10444863
Chromosome Location	chr15:78358837-78358838
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	EP300	chr15:78357739-78358842	GM12878	blood:	n/a	n/a
2	CHD1	chr15:78357637-78359294	GM12878	blood:	n/a	n/a
3	IRF4	chr15:78358298-78358875	GM12878	blood:	n/a	n/a
4	YY1	chr15:78358275-78358876	GM12878	blood:	n/a	n/a
5	BATF	chr15:78358385-78358895	GM12878	blood:	n/a	n/a
6	RCOR1	chr15:78358158-78358856	GM12878	blood:	n/a	n/a
7	RUNX3	chr15:78357534-78358994	GM12878	blood:	n/a	n/a
8	FOXA1	chr15:78358834-78359248	HepG2	liver:	n/a	chr15:78359037-78359052
9	POLR2A	chr15:78358352-78358864	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:78357600-78358998	GM12878	blood:	n/a	n/a
11	RUNX3	chr15:78357443-78358958	GM12878	blood:	n/a	n/a
12	SMC3	chr15:78358437-78358910	GM12878	blood:	n/a	n/a
13	STAT3	chr15:78358313-78358874	GM12878	blood:	n/a	n/a
14	TCF7L2	chr15:78358752-78359414	PANC-1	pancreas:	n/a	n/a
15	ATF2	chr15:78358243-78358904	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:78358202-78359038	GM12892	blood:	n/a	n/a
17	CUX1	chr15:78358081-78358942	GM12878	blood:	n/a	n/a
18	BCLAF1	chr15:78358238-78358883	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:78357377-78359359	GM12891	blood:	n/a	n/a
20	POLR2A	chr15:78357953-78358900	Raji	blood:	n/a	n/a
21	POU2F2	chr15:78358289-78358913	GM12891	blood:	n/a	chr15:78358584-78358598 chr15:78358586-78358598
22	POLR2A	chr15:78358369-78358868	GM12878	blood:	n/a	n/a
23	TAF1	chr15:78358309-78358843	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:78358277-78358896	GM12891	blood:	n/a	n/a
25	IKZF1	chr15:78357593-78359020	GM12878	blood:	n/a	chr15:78358173-78358181
26	MAFK	chr15:78358787-78359089	HepG2	liver:	n/a	n/a
27	YY1	chr15:78358334-78358861	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:78357492-78359020	GM12892	blood:	n/a	n/a
29	PAX5	chr15:78358239-78358931	GM12878	blood:	n/a	chr15:78358643-78358661
30	BCLAF1	chr15:78358124-78358842	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:78357495-78358959	GM12878	blood:	n/a	n/a
32	EP300	chr15:78358540-78361397	SK-N-SH	brain:	n/a	chr15:78360191-78360205 chr15:78361188-78361198 chr15:78360535-78360543
33	POLR2A	chr15:78358220-78358977	GM12891	blood:	n/a	n/a
34	NFIC	chr15:78357506-78359050	GM12878	blood:	n/a	n/a
35	MXI1	chr15:78358329-78359078	GM12878	blood:	n/a	n/a
36	MTA3	chr15:78357283-78358986	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:78358229-78359009	GM12878	blood:	n/a	n/a
38	EP300	chr15:78358077-78358907	GM12878	blood:	n/a	n/a
39	WRNIP1	chr15:78357750-78359278	GM12878	blood:	n/a	n/a
40	POLR2A	chr15:78358303-78358918	GM12891	blood:	n/a	n/a
41	POLR2A	chr15:78358821-78359312	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr15:78358324-78358990	GM12891	blood:	n/a	n/a
43	POU2F2	chr15:78358288-78358876	GM12878	blood:	n/a	chr15:78358584-78358598 chr15:78358586-78358598
44	POLR2A	chr15:78358226-78358912	GM12892	blood:	n/a	n/a
45	POU2F2	chr15:78358273-78358921	GM12891	blood:	n/a	chr15:78358584-78358598 chr15:78358586-78358598
46	POLR2A	chr15:78357532-78358927	GM12878	blood:	n/a	n/a
47	YY1	chr15:78358303-78358914	GM12892	blood:	n/a	n/a
48	POLR2A	chr15:78358290-78358958	GM12892	blood:	n/a	n/a
49	TBP	chr15:78358320-78358868	GM12878	blood:	n/a	n/a
50	FOXA1	chr15:78358821-78359238	HepG2	liver:	n/a	chr15:78359037-78359052

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78357496..78359399-chr15:78368822..78370574,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78357257-78359670	l_1195_chr15:78344341-78421177_testes

Variant related genes	Relation type
TBC1D2B	TF binding region
ENSG00000167202	Chromatin interaction
ENSG00000183476	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10519181	0.84[CEU][hapmap]
rs12593545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1442293	0.85[CEU][hapmap]
rs16969422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17477813	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1837913	0.84[CEU][hapmap]
rs2044099	0.84[CEU][hapmap]
rs35472584	0.88[CEU][hapmap]
rs4886989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56357772	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs872926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs894301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78344800-78359800	Weak transcription	Fetal Brain Female	brain
2	chr15:78347400-78367800	Enhancers	Placenta	Placenta
3	chr15:78349400-78360800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:78354200-78359600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr15:78354200-78360600	Enhancers	Colon Smooth Muscle	Colon
6	chr15:78354200-78363200	Enhancers	Fetal Intestine Large	intestine
7	chr15:78354200-78363200	Enhancers	Stomach Mucosa	stomach
8	chr15:78354200-78366400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:78354600-78365400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr15:78354600-78366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:78354800-78359600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr15:78354800-78359800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:78354800-78360800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:78354800-78360800	Enhancers	Brain Anterior Caudate	brain
15	chr15:78354800-78362600	Enhancers	Fetal Kidney	kidney
16	chr15:78354800-78362800	Enhancers	HSMMtube	muscle
17	chr15:78355000-78360800	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr15:78355000-78363200	Enhancers	Brain Substantia Nigra	brain
19	chr15:78355200-78360800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:78355200-78362800	Enhancers	Pancreas	Pancrea
21	chr15:78355200-78364000	Enhancers	Dnd41	blood
22	chr15:78355400-78359800	Weak transcription	Brain Germinal Matrix	brain
23	chr15:78355600-78365400	Enhancers	Small Intestine	intestine
24	chr15:78355800-78360800	Enhancers	Rectal Smooth Muscle	rectum
25	chr15:78355800-78363000	Enhancers	Spleen	Spleen
26	chr15:78355800-78363200	Enhancers	Right Atrium	heart
27	chr15:78355800-78364000	Enhancers	Fetal Muscle Leg	muscle
28	chr15:78356000-78363000	Enhancers	Brain Angular Gyrus	brain
29	chr15:78356000-78363800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:78356200-78362800	Enhancers	Psoas Muscle	Psoas
31	chr15:78356200-78363000	Enhancers	Fetal Stomach	stomach
32	chr15:78356400-78361000	Enhancers	HUVEC	blood vessel
33	chr15:78356400-78363000	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:78356600-78359600	Weak transcription	Ovary	ovary
35	chr15:78356600-78360800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr15:78356600-78362400	Enhancers	Fetal Lung	lung
37	chr15:78356800-78359800	Weak transcription	Fetal Brain Male	brain
38	chr15:78357000-78359400	Flanking Active TSS	GM12878-XiMat	blood
39	chr15:78357000-78361000	Enhancers	Primary hematopoietic stem cells	blood
40	chr15:78357000-78363200	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr15:78357200-78359000	Enhancers	Esophagus	oesophagus
42	chr15:78357200-78360800	Enhancers	Primary B cells from cord blood	blood
43	chr15:78357200-78363000	Enhancers	Primary B cells from peripheral blood	blood
44	chr15:78357400-78359000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:78357400-78359800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr15:78357400-78361200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:78357400-78361200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:78357400-78361800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:78357400-78364400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:78357400-78365000	Enhancers	Sigmoid Colon	Sigmoid Colon

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