Variant report

Variant	rs17819300
Chromosome Location	chr15:56210929-56210930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56209638..56212268-chr15:56534926..56537157,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151575	Chromatin interaction
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11550869	1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[TSI][hapmap]
rs12898553	0.89[ASN][1000 genomes]
rs12902644	0.85[JPT][hapmap]
rs17238461	1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[TSI][hapmap]
rs17238482	0.89[ASN][1000 genomes]
rs17238489	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17819282	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136386	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2175104	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4774833	0.85[JPT][hapmap]
rs55782406	0.85[ASN][1000 genomes]
rs55858643	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55908996	0.85[EUR][1000 genomes]
rs55999037	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56109562	0.85[EUR][1000 genomes]
rs56339902	0.85[EUR][1000 genomes]
rs62043760	0.87[ASN][1000 genomes]
rs62043761	0.87[ASN][1000 genomes]
rs62043763	0.89[ASN][1000 genomes]
rs62043764	0.89[ASN][1000 genomes]
rs62043792	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62043793	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62043796	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62043801	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62043802	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62043810	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62043815	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62043816	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62043847	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62043854	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62043858	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62045161	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62045162	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62045163	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62045164	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62045205	0.90[EUR][1000 genomes]
rs62045207	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62045208	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62045219	0.85[EUR][1000 genomes]
rs62046648	0.85[ASN][1000 genomes]
rs62046649	0.85[ASN][1000 genomes]
rs62046650	0.85[ASN][1000 genomes]
rs7174459	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569542	chr15:56185262-56210929	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Brain connectivity	23471985	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17819300	CAV2	trans	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56176000-56216200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:56188600-56218400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:56190000-56220000	Weak transcription	Pancreas	Pancrea
4	chr15:56190200-56221200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:56190400-56219800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:56200200-56213200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:56200800-56218000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
9	chr15:56201200-56217200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:56206800-56217800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:56207600-56221200	Weak transcription	Right Ventricle	heart
12	chr15:56208600-56218000	Weak transcription	Esophagus	oesophagus
13	chr15:56208800-56221600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:56208800-56230000	Weak transcription	Liver	Liver
15	chr15:56209000-56218400	Weak transcription	Fetal Stomach	stomach
16	chr15:56209000-56230400	Weak transcription	Primary T cells from cord blood	blood
17	chr15:56209200-56221200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:56209200-56221600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:56209200-56230200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:56209200-56230200	Weak transcription	Aorta	Aorta
21	chr15:56209400-56211800	Enhancers	Hela-S3	cervix
22	chr15:56209600-56211000	Enhancers	NHEK	skin
23	chr15:56209600-56216200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:56209600-56230800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:56209600-56247400	Weak transcription	Psoas Muscle	Psoas
26	chr15:56209800-56211000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr15:56210000-56211000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:56210000-56211000	Enhancers	NHLF	lung
29	chr15:56210000-56216400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:56210200-56211600	Enhancers	A549	lung
31	chr15:56210200-56221600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:56210200-56229600	Weak transcription	HSMMtube	muscle
33	chr15:56210200-56229800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:56210400-56211000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:56210600-56212600	Weak transcription	HMEC	breast
36	chr15:56210800-56212400	Weak transcription	NHDF-Ad	bronchial
37	chr15:56210800-56228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:56210800-56229200	Weak transcription	HUVEC	blood vessel

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