Variant report

Variant	rs3011777
Chromosome Location	chr10:52285511-52285512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52285415..52288403-chr10:52289940..52291590,2	K562	blood:
2	chr10:52177517..52180789-chr10:52285364..52288556,3	K562	blood:
3	chr10:52117604..52119516-chr10:52283791..52286665,2	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1010930	0.88[ASN][1000 genomes]
rs10490963	0.84[ASW][hapmap]
rs10763535	0.89[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10763550	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs10763560	0.90[CHB][hapmap]
rs10763566	0.86[CHB][hapmap]
rs10826149	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10826155	0.90[ASN][1000 genomes]
rs10826159	0.87[ASN][1000 genomes]
rs10826160	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10826161	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10826163	0.88[ASN][1000 genomes]
rs10826164	0.88[ASN][1000 genomes]
rs10826165	0.88[ASN][1000 genomes]
rs10826166	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10826167	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10826170	0.83[ASN][1000 genomes]
rs11006084	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11006114	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11006118	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11006141	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11006160	0.80[ASN][1000 genomes]
rs11006201	0.81[ASN][1000 genomes]
rs11006217	0.81[CHB][hapmap]
rs12415817	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12415836	0.88[ASN][1000 genomes]
rs12572387	0.86[CHB][hapmap]
rs17518471	0.84[ASW][hapmap]
rs17519380	0.84[ASW][hapmap]
rs1884570	0.88[ASN][1000 genomes]
rs1916569	0.84[ASW][hapmap]
rs2144861	0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2224249	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs34659292	0.88[ASN][1000 genomes]
rs34672995	0.84[ASW][hapmap]
rs36122110	0.88[ASN][1000 genomes]
rs3802537	0.84[ASW][hapmap]
rs4935173	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4935174	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4935733	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7074764	0.86[CHB][hapmap]
rs7078284	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7088141	0.86[CHB][hapmap]
rs7094143	0.88[ASN][1000 genomes]
rs7893884	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7900424	0.90[CHB][hapmap]
rs7907260	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7915606	0.91[CHB][hapmap]
rs7916397	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9299582	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9919413	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3011777	PRKG1	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr10:52271600-52300600	Weak transcription	Aorta	Aorta
3	chr10:52272600-52302800	Weak transcription	Fetal Stomach	stomach
4	chr10:52272800-52288200	Weak transcription	HSMMtube	muscle
5	chr10:52273200-52285800	Weak transcription	K562	blood
6	chr10:52273200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr10:52273200-52287400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:52273200-52288400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:52273400-52286000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:52273400-52287000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:52273400-52287200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:52273600-52286800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr10:52273600-52287400	Weak transcription	GM12878-XiMat	blood
14	chr10:52273600-52289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr10:52273600-52298400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:52273600-52299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr10:52274000-52287200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:52274800-52288200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr10:52275200-52294200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:52275600-52286800	Weak transcription	Pancreas	Pancrea
21	chr10:52276200-52286200	Weak transcription	Fetal Heart	heart
22	chr10:52279400-52298200	Weak transcription	Fetal Intestine Small	intestine
23	chr10:52279600-52286600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:52279600-52286800	Weak transcription	Left Ventricle	heart
25	chr10:52279600-52290000	Weak transcription	Primary B cells from cord blood	blood
26	chr10:52279600-52298400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr10:52279600-52298400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr10:52279600-52298800	Weak transcription	Lung	lung
29	chr10:52279800-52286400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:52279800-52286800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr10:52279800-52287200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:52279800-52298600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:52282200-52286200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr10:52282200-52286400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr10:52282400-52285600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr10:52282600-52285800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:52282800-52291200	Weak transcription	Esophagus	oesophagus
39	chr10:52282800-52301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr10:52283000-52300400	Weak transcription	Psoas Muscle	Psoas
41	chr10:52283400-52286000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:52283600-52288200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr10:52283800-52287200	Weak transcription	Right Atrium	heart
44	chr10:52283800-52288600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr10:52284200-52286000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr10:52284200-52287000	Weak transcription	Primary T cells from cord blood	blood
47	chr10:52284200-52287000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr10:52284400-52292400	Weak transcription	Brain Angular Gyrus	brain
49	chr10:52284600-52287200	Weak transcription	Brain Anterior Caudate	brain
50	chr10:52284600-52287200	Weak transcription	Brain Cingulate Gyrus	brain

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