Variant report

Variant	rs4776020
Chromosome Location	chr15:52509673-52509674
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	CTCF	chr15:52509381-52509696	GM19240	blood:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
2	RAD21	chr15:52509376-52509729	ECC-1	luminal epithelium:	n/a	chr15:52509508-52509527
3	CTCF	chr15:52509277-52509834	MCF-7	breast:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
4	CTCF	chr15:52509384-52509677	NHEK	skin:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
5	CTCF	chr15:52509421-52509699	K562	blood:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
6	RAD21	chr15:52509340-52509677	GM12878	blood:	n/a	chr15:52509508-52509527
7	SMC3	chr15:52509373-52509686	K562	blood:	n/a	chr15:52509509-52509523
8	NFYB	chr15:52509560-52509699	GM12878	blood:	n/a	n/a
9	CTCF	chr15:52509302-52509727	GM12878	blood:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
10	RAD21	chr15:52509369-52509701	H1-hESC	embryonic stem cell:	n/a	chr15:52509508-52509527
11	RAD21	chr15:52509368-52509720	H1-hESC	embryonic stem cell:	n/a	chr15:52509508-52509527
12	RAD21	chr15:52509351-52509692	HepG2	liver:	n/a	chr15:52509508-52509527
13	CTCF	chr15:52509256-52509696	MCF-7	breast:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
14	RAD21	chr15:52509208-52509840	A549	lung:	n/a	chr15:52509508-52509527
15	CTCF	chr15:52509386-52509674	MCF-7	breast:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
16	ZNF143	chr15:52509373-52509702	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr15:52509656-52509682	K562	blood:	n/a	n/a
18	RAD21	chr15:52509327-52509787	A549	lung:	n/a	chr15:52509508-52509527
19	RAD21	chr15:52509348-52509704	GM12878	blood:	n/a	chr15:52509508-52509527
20	CTCF	chr15:52509395-52509676	GM19238	blood:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
21	ZNF384	chr15:52509618-52509674	K562	blood:	n/a	n/a
22	SMC3	chr15:52509351-52509705	GM12878	blood:	n/a	chr15:52509509-52509523
23	USF1	chr15:52509453-52509727	K562	blood:	n/a	n/a
24	CTCF	chr15:52509260-52509811	K562	blood:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
25	CTCF	chr15:52509284-52509731	A549	lung:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
26	POLR2A	chr15:52509523-52509692	HepG2	liver:	n/a	n/a
27	RAD21	chr15:52509257-52509766	HCT-116	colon:	n/a	chr15:52509508-52509527
28	MAX	chr15:52509425-52509766	NB4	blood:	n/a	chr15:52509601-52509611
29	E2F6	chr15:52509612-52509746	K562	blood:	n/a	n/a
30	CTCF	chr15:52509361-52509691	H1-hESC	embryonic stem cell:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
31	RCOR1	chr15:52509372-52509718	K562	blood:	n/a	n/a
32	MAX	chr15:52509365-52509855	K562	blood:	n/a	chr15:52509601-52509611
33	CTCF	chr15:52509307-52509693	H1-hESC	embryonic stem cell:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524
34	HCFC1	chr15:52509398-52509681	K562	blood:	n/a	n/a
35	MAX	chr15:52509475-52509770	K562	blood:	n/a	chr15:52509601-52509611
36	POLR2A	chr15:52509671-52509708	MCF-7	breast:	n/a	n/a
37	NFE2	chr15:52509615-52509704	GM12878	blood:	n/a	chr15:52509661-52509671
38	CTCF	chr15:52509340-52509713	K562	blood:	n/a	chr15:52509509-52509530 chr15:52509507-52509525 chr15:52509510-52509523 chr15:52509510-52509523 chr15:52509508-52509524

No.	Distal block	Cell Line	Cell type
1	chr15:52500676..52501391-chr15:52509036..52509975,2	K562	blood:
2	chr15:52475563..52476065-chr15:52509089..52509975,2	MCF-7	breast:
3	chr15:52509083..52509697-chr15:53027309..53027962,2	MCF-7	breast:
4	chr15:52509010..52510015-chr15:52519316..52520083,4	MCF-7	breast:
5	chr15:52505827..52511235-chr15:52516876..52519875,7	MCF-7	breast:
6	chr15:52508008..52509939-chr15:53026331..53028847,2	MCF-7	breast:
7	chr15:52509233..52510844-chr15:52512535..52515103,2	K562	blood:
8	chr15:52509089..52509941-chr15:53027516..53028325,2	MCF-7	breast:
9	chr15:52509455..52510001-chr15:52755530..52756071,2	MCF-7	breast:

Variant related genes	Relation type
MYO5C	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11070889	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs16964751	1.00[CEU][hapmap]
rs16964760	0.81[EUR][1000 genomes]
rs17540546	1.00[CEU][hapmap]
rs17540734	1.00[CEU][hapmap]
rs17541016	0.92[TSI][hapmap]
rs17612637	1.00[CEU][hapmap]
rs17612796	1.00[CEU][hapmap]
rs2414134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4776018	1.00[CEU][hapmap]
rs6493536	1.00[CEU][hapmap]
rs6493537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7168334	1.00[CEU][hapmap]
rs7177057	0.88[EUR][1000 genomes]
rs74015635	0.94[EUR][1000 genomes]
rs754658	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8024892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8034075	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4776020	GNB5	cis	multi-tissue	Pritchard

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52495600-52519000	Strong transcription	HepG2	liver
8	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
13	chr15:52499200-52512600	Strong transcription	A549	lung
14	chr15:52500000-52512000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr15:52501400-52512400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:52501600-52519000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
20	chr15:52502000-52519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:52502000-52523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:52502400-52520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:52502600-52519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:52502800-52517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr15:52503200-52512400	Strong transcription	Primary hematopoietic stem cells	blood
26	chr15:52503200-52519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:52504400-52512600	Weak transcription	Placenta	Placenta
28	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
29	chr15:52505600-52525600	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:52505800-52513000	Weak transcription	Primary T cells from cord blood	blood
32	chr15:52506000-52510000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:52506000-52516400	Weak transcription	Spleen	Spleen
34	chr15:52506200-52512600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:52506400-52514600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
37	chr15:52508200-52513000	Strong transcription	Fetal Intestine Small	intestine
38	chr15:52508600-52518800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr15:52508600-52519000	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:52508800-52510600	Strong transcription	Stomach Mucosa	stomach
41	chr15:52508800-52511600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:52509000-52509800	Enhancers	Psoas Muscle	Psoas
43	chr15:52509000-52509800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:52509000-52510400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:52509000-52510400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:52509000-52510400	Strong transcription	Adipose Nuclei	Adipose
47	chr15:52509000-52511800	Strong transcription	Esophagus	oesophagus
48	chr15:52509000-52511800	Strong transcription	Gastric	stomach
49	chr15:52509000-52511800	Strong transcription	Pancreas	Pancrea
50	chr15:52509000-52512000	Strong transcription	Fetal Muscle Trunk	muscle

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