Variant report

Variant	rs10500279
Chromosome Location	chr19:39035068-39035069
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39033172..39036412-chr19:39037332..39039835,4	K562	blood:
2	chr19:39034757..39035681-chr19:39124986..39126314,5	K562	blood:
3	chr19:38996233..38998057-chr19:39033853..39035583,2	K562	blood:
4	chr19:39033486..39035242-chr19:39166999..39169094,2	K562	blood:
5	chr19:39034731..39035402-chr19:39127286..39128111,2	K562	blood:
6	chr19:39034364..39037284-chr19:39108616..39110630,2	K562	blood:
7	chr19:39033262..39037138-chr19:39114289..39118400,4	K562	blood:
8	chr19:39033816..39036300-chr19:39320862..39322529,2	MCF-7	breast:
9	chr19:39033355..39037027-chr19:39040774..39043679,3	K562	blood:
10	chr19:39033772..39036275-chr19:39124908..39126988,2	MCF-7	breast:
11	chr19:39034798..39036647-chr19:39056584..39059105,2	MCF-7	breast:
12	chr19:39033295..39037284-chr19:39108058..39111883,5	K562	blood:
13	chr19:39033468..39036345-chr19:39125493..39127888,3	K562	blood:
14	chr19:39033406..39035979-chr19:39137049..39139555,4	MCF-7	breast:
15	chr19:39033844..39036603-chr19:39138294..39139887,2	K562	blood:
16	chr19:39033384..39036751-chr19:39123967..39127917,4	K562	blood:
17	chr19:39034875..39035594-chr19:39260160..39260978,2	K562	blood:
18	chr19:39033166..39035444-chr19:39222579..39224639,2	K562	blood:
19	chr19:39033978..39035900-chr19:39338970..39341191,3	MCF-7	breast:
20	chr19:39015321..39017882-chr19:39033262..39036182,2	K562	blood:
21	chr19:39034756..39035696-chr19:39125402..39126211,3	MCF-7	breast:
22	chr19:38997702..38999561-chr19:39033477..39036015,2	MCF-7	breast:
23	chr19:39014964..39016821-chr19:39033783..39036182,2	K562	blood:
24	chr19:39034696..39035517-chr19:39420545..39421446,2	K562	blood:
25	chr19:39034770..39036349-chr19:39131227..39134089,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000128626	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000196218	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11881082	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17722095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17722101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071088	0.88[CEU][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs2945047	0.96[ASN][1000 genomes]
rs41274330	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58611824	0.96[ASN][1000 genomes]
rs58875004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59591700	0.86[ASN][1000 genomes]
rs60909679	0.96[ASN][1000 genomes]
rs61441471	0.97[ASN][1000 genomes]
rs73031001	0.92[ASN][1000 genomes]
rs73032604	0.97[ASN][1000 genomes]
rs73032616	0.97[ASN][1000 genomes]
rs73032620	0.97[ASN][1000 genomes]
rs73032625	0.97[ASN][1000 genomes]
rs73032627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032639	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73032648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs892052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs908644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv1058902	chr19:39025940-39078574	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1064490	chr19:39029788-39078574	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10500279	RYR1	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
2	chr19:39026000-39052400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:39028400-39035200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr19:39029000-39051600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr19:39029600-39046000	Weak transcription	HSMM	muscle
6	chr19:39029800-39035200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:39030000-39035200	Weak transcription	Primary T cells from cord blood	blood
8	chr19:39030000-39054600	Strong transcription	Fetal Muscle Leg	muscle
9	chr19:39030200-39035200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:39030200-39055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:39033600-39036600	Strong transcription	HSMMtube	muscle
12	chr19:39034200-39035200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:39034200-39035200	Enhancers	Spleen	Spleen
14	chr19:39034200-39036000	Enhancers	Placenta	Placenta
15	chr19:39034200-39036200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:39034400-39035200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr19:39034400-39035200	Flanking Active TSS	HepG2	liver
18	chr19:39034400-39035400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:39034400-39035400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr19:39034400-39035400	Flanking Active TSS	Brain Anterior Caudate	brain
21	chr19:39034400-39035400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:39034400-39035400	Enhancers	Pancreas	Pancrea
23	chr19:39034400-39035600	Enhancers	Liver	Liver
24	chr19:39034400-39035600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
25	chr19:39034400-39035600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr19:39034400-39035800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr19:39034400-39036000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr19:39034600-39035200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:39034600-39035200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:39034600-39035200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:39034600-39035200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr19:39034600-39035400	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr19:39034600-39035600	Enhancers	Primary B cells from cord blood	blood
34	chr19:39034600-39035600	Flanking Active TSS	GM12878-XiMat	blood
35	chr19:39034600-39035800	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:39034600-39035800	Enhancers	Primary hematopoietic stem cells	blood
37	chr19:39034600-39035800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr19:39034600-39035800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr19:39034600-39035800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:39034600-39035800	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:39034600-39035800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:39034600-39035800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:39034600-39035800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:39034600-39036000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr19:39034600-39036000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr19:39034600-39036200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:39034600-39051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:39034800-39035200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr19:39034800-39035200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr19:39034800-39035200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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