Variant report

Variant	rs2175104
Chromosome Location	chr15:56228676-56228677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56221865..56223584-chr15:56227077..56228974,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12902644	0.85[JPT][hapmap]
rs17819282	0.83[EUR][1000 genomes]
rs17819300	1.00[ASW][hapmap];0.85[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2136386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774833	0.85[JPT][hapmap]
rs55858643	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55908996	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55999037	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56109562	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56339902	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62043810	0.83[EUR][1000 genomes]
rs62043815	0.83[EUR][1000 genomes]
rs62043816	0.83[EUR][1000 genomes]
rs62043847	0.85[EUR][1000 genomes]
rs62043854	0.88[EUR][1000 genomes]
rs62043858	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62045161	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62045205	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62045207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62045208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62045211	0.91[ASN][1000 genomes]
rs62045219	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62045225	0.89[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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2175104	CAV2	trans	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56201000-56230000	Weak transcription	Fetal Intestine Large	intestine
2	chr15:56208800-56230000	Weak transcription	Liver	Liver
3	chr15:56209000-56230400	Weak transcription	Primary T cells from cord blood	blood
4	chr15:56209200-56230200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:56209200-56230200	Weak transcription	Aorta	Aorta
6	chr15:56209600-56230800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:56209600-56247400	Weak transcription	Psoas Muscle	Psoas
8	chr15:56210200-56229600	Weak transcription	HSMMtube	muscle
9	chr15:56210200-56229800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:56210800-56228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:56210800-56229200	Weak transcription	HUVEC	blood vessel
12	chr15:56211400-56230800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:56211600-56229400	Weak transcription	A549	lung
14	chr15:56211800-56242400	Weak transcription	Hela-S3	cervix
15	chr15:56216800-56230000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:56217200-56230000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:56218800-56230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:56219200-56230200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:56221600-56242400	Weak transcription	NHEK	skin
20	chr15:56221800-56229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:56221800-56230200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:56222200-56234200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:56224000-56230000	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:56225800-56229200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:56226200-56245800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:56227400-56230600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:56227600-56228800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:56227600-56229200	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:56227800-56229400	Weak transcription	NHLF	lung
30	chr15:56228200-56230000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr15:56228600-56230600	Weak transcription	Fetal Lung	lung

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