Variant report

Variant	rs16964764
Chromosome Location	chr15:52496933-52496934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52496666..52498415-chr15:52943182..52945600,2	MCF-7	breast:
2	chr15:52490583..52493341-chr15:52495690..52497314,2	MCF-7	breast:
3	chr15:52477453..52480086-chr15:52495513..52498158,2	K562	blood:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16964751	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16964760	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17540546	0.94[AMR][1000 genomes]
rs17540734	0.93[AMR][1000 genomes]
rs17612637	1.00[AMR][1000 genomes]
rs17612796	1.00[AMR][1000 genomes]
rs2231289	1.00[AMR][1000 genomes]
rs35581121	1.00[AMR][1000 genomes]
rs41277704	0.94[AMR][1000 genomes]
rs41277706	0.94[AMR][1000 genomes]
rs41277712	0.87[AMR][1000 genomes]
rs4776006	1.00[AMR][1000 genomes]
rs4776018	0.87[AMR][1000 genomes]
rs4776019	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62016465	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62016466	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7168334	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7177057	0.88[AFR][1000 genomes]
rs7181736	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74015635	0.83[AMR][1000 genomes]
rs8024846	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16964764	GNB5	cis	multi-tissue	Pritchard
rs16964764	GNB5	cis	lymphoblastoid	seeQTL
rs16964764	RNF130	trans	lymphoblastoid	seeQTL

Chromatin state (count:69 , 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	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52477600-52497000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:52477600-52497200	Weak transcription	Stomach Mucosa	stomach
6	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
7	chr15:52483800-52497000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:52484200-52497000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:52484200-52498600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:52484200-52503200	Weak transcription	Lung	lung
11	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
13	chr15:52487400-52505200	Weak transcription	Thymus	Thymus
14	chr15:52488600-52497000	Weak transcription	Aorta	Aorta
15	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:52488800-52505600	Weak transcription	Fetal Kidney	kidney
17	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:52490400-52503000	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:52494600-52499200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:52495400-52497800	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr15:52495400-52500600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:52495600-52519000	Strong transcription	HepG2	liver
24	chr15:52495800-52498600	Weak transcription	Right Atrium	heart
25	chr15:52495800-52499200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr15:52496000-52497400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:52496000-52497600	Strong transcription	Colonic Mucosa	Colon
28	chr15:52496000-52497600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr15:52496000-52497800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52496000-52498000	Strong transcription	Gastric	stomach
31	chr15:52496000-52498200	Strong transcription	Primary hematopoietic stem cells	blood
32	chr15:52496000-52498400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:52496000-52498400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:52496000-52498600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:52496000-52499000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr15:52496000-52500800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:52496000-52505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:52496200-52497400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:52496200-52497400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:52496200-52497400	Strong transcription	A549	lung
41	chr15:52496200-52497600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr15:52496200-52497600	Strong transcription	Liver	Liver
43	chr15:52496200-52497600	Strong transcription	Fetal Intestine Large	intestine
44	chr15:52496200-52497600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:52496200-52497600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:52496200-52497800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:52496200-52497800	Strong transcription	Duodenum Mucosa	Duodenum
48	chr15:52496200-52499200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:52496200-52500200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:52496200-52501600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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