Variant report

Variant	rs17477813
Chromosome Location	chr15:78360691-78360692
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	KAP1	chr15:78359577-78361389	HEK293	kidney:	n/a	n/a
2	BHLHE40	chr15:78360523-78361474	GM12878	blood:	n/a	n/a
3	MAFK	chr15:78360181-78360878	IMR90	lung:	n/a	n/a
4	RUNX3	chr15:78360533-78361475	GM12878	blood:	n/a	n/a
5	MYC	chr15:78360643-78360837	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr15:78360590-78360862	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr15:78360473-78362556	GM12878	blood:	n/a	n/a
8	NFIC	chr15:78359451-78361108	SK-N-SH	brain:	n/a	n/a
9	EBF1	chr15:78360656-78361310	GM12878	blood:	n/a	chr15:78361016-78361026 chr15:78361017-78361026 chr15:78361017-78361026 chr15:78361015-78361026 chr15:78361015-78361028
10	GATA3	chr15:78359413-78361164	SK-N-SH	brain:	n/a	chr15:78360539-78360546
11	MTA3	chr15:78360505-78361548	GM12878	blood:	n/a	n/a
12	TCF12	chr15:78359394-78361102	SK-N-SH	brain:	n/a	chr15:78361078-78361087
13	EBF1	chr15:78360616-78361611	GM12878	blood:	n/a	chr15:78361016-78361026 chr15:78361017-78361026 chr15:78361017-78361026 chr15:78361015-78361026 chr15:78361015-78361028
14	GATA3	chr15:78359506-78361013	SK-N-SH	brain:	n/a	chr15:78360539-78360546
15	EP300	chr15:78358540-78361397	SK-N-SH	brain:	n/a	chr15:78360191-78360205 chr15:78361188-78361198 chr15:78360535-78360543
16	TBL1XR1	chr15:78360554-78361659	GM12878	blood:	n/a	n/a
17	BCLAF1	chr15:78360529-78361416	GM12878	blood:	n/a	n/a
18	TCF12	chr15:78359500-78360886	SK-N-SH	brain:	n/a	n/a
19	MAX	chr15:78360624-78362634	GM12878	blood:	n/a	chr15:78361366-78361376
20	RUNX3	chr15:78360561-78361640	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78360126..78361739-chr15:78367541..78369302,2	K562	blood:

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1004855	0.88[CEU][hapmap]
rs10444863	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs1053506	0.84[YRI][hapmap]
rs10775214	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs11072726	0.81[ASW][hapmap]
rs11631578	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs11633569	0.80[AFR][1000 genomes]
rs11634607	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs11636889	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs12591418	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs12593545	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs12594823	0.82[ASW][hapmap]
rs12898535	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs12900731	0.93[ASW][hapmap];0.85[YRI][hapmap]
rs12907701	0.81[AMR][1000 genomes]
rs12907814	0.81[AMR][1000 genomes]
rs12911332	0.91[CEU][hapmap]
rs12915731	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs12915847	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs1348256	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs16969422	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1837912	0.93[ASW][hapmap];0.83[LWK][hapmap]
rs2015951	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs2044100	0.82[AFR][1000 genomes]
rs4243073	0.87[AFR][1000 genomes]
rs4886552	0.82[AFR][1000 genomes]
rs4886553	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs4886554	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs4886556	0.82[AFR][1000 genomes]
rs4886987	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs4886989	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4886991	0.85[YRI][hapmap]
rs4886992	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs4886993	0.85[YRI][hapmap]
rs4886997	0.82[AFR][1000 genomes]
rs4886998	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs4886999	0.88[CEU][hapmap];0.82[MEX][hapmap]
rs4887001	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs4887002	0.80[AFR][1000 genomes]
rs56357772	0.83[ASN][1000 genomes]
rs7169882	0.82[AFR][1000 genomes]
rs7170101	0.93[ASW][hapmap];0.85[YRI][hapmap]
rs7170286	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs7170452	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs7170746	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs7173128	0.88[CEU][hapmap];0.86[MEX][hapmap]
rs7175192	0.80[AFR][1000 genomes]
rs7181594	0.81[AMR][1000 genomes]
rs8025423	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs8033216	0.93[ASW][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs872926	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs894295	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs894296	0.82[AFR][1000 genomes]
rs894301	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[ASN][1000 genomes]
rs894302	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs9788640	0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs9920180	0.93[ASW][hapmap];0.85[YRI][hapmap]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17477813	MORF4L1	cis	parietal	SCAN
rs17477813	BBS4	cis	cerebellum	SCAN
rs17477813	HEXA	cis	parietal	SCAN
rs17477813	ISL2	cis	parietal	SCAN
rs17477813	PSTPIP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78347400-78367800	Enhancers	Placenta	Placenta
2	chr15:78349400-78360800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:78354200-78363200	Enhancers	Fetal Intestine Large	intestine
4	chr15:78354200-78363200	Enhancers	Stomach Mucosa	stomach
5	chr15:78354200-78366400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:78354600-78365400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr15:78354600-78366400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:78354800-78360800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:78354800-78360800	Enhancers	Brain Anterior Caudate	brain
10	chr15:78354800-78362600	Enhancers	Fetal Kidney	kidney
11	chr15:78354800-78362800	Enhancers	HSMMtube	muscle
12	chr15:78355000-78360800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr15:78355000-78363200	Enhancers	Brain Substantia Nigra	brain
14	chr15:78355200-78360800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:78355200-78362800	Enhancers	Pancreas	Pancrea
16	chr15:78355200-78364000	Enhancers	Dnd41	blood
17	chr15:78355600-78365400	Enhancers	Small Intestine	intestine
18	chr15:78355800-78360800	Enhancers	Rectal Smooth Muscle	rectum
19	chr15:78355800-78363000	Enhancers	Spleen	Spleen
20	chr15:78355800-78363200	Enhancers	Right Atrium	heart
21	chr15:78355800-78364000	Enhancers	Fetal Muscle Leg	muscle
22	chr15:78356000-78363000	Enhancers	Brain Angular Gyrus	brain
23	chr15:78356000-78363800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:78356200-78362800	Enhancers	Psoas Muscle	Psoas
25	chr15:78356200-78363000	Enhancers	Fetal Stomach	stomach
26	chr15:78356400-78361000	Enhancers	HUVEC	blood vessel
27	chr15:78356400-78363000	Enhancers	Brain Cingulate Gyrus	brain
28	chr15:78356600-78360800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr15:78356600-78362400	Enhancers	Fetal Lung	lung
30	chr15:78357000-78361000	Enhancers	Primary hematopoietic stem cells	blood
31	chr15:78357000-78363200	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr15:78357200-78360800	Enhancers	Primary B cells from cord blood	blood
33	chr15:78357200-78363000	Enhancers	Primary B cells from peripheral blood	blood
34	chr15:78357400-78361200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:78357400-78361200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:78357400-78361800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:78357400-78364400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:78357400-78365000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr15:78357600-78362800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr15:78357600-78362800	Enhancers	Gastric	stomach
41	chr15:78357600-78363000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr15:78357600-78365200	Enhancers	Lung	lung
43	chr15:78357800-78360800	Enhancers	NHDF-Ad	bronchial
44	chr15:78357800-78361600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:78357800-78361600	Enhancers	Aorta	Aorta
46	chr15:78358000-78360800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:78358000-78360800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:78358000-78361000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:78358000-78361400	Enhancers	Thymus	Thymus
50	chr15:78358000-78362800	Enhancers	HUES48 Cell Line	embryonic stem cell

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