Variant report

Variant	rs58052451
Chromosome Location	chr7:6325205-6325206
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	chr7:6310704..6313197-chr7:6323123..6325824,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008256	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10216296	0.89[EUR][1000 genomes]
rs10227013	0.93[ASN][1000 genomes]
rs10229323	0.80[ASN][1000 genomes]
rs10235115	1.00[ASN][1000 genomes]
rs10240510	1.00[ASN][1000 genomes]
rs10245186	0.82[ASN][1000 genomes]
rs10261217	0.93[ASN][1000 genomes]
rs10263878	0.82[ASN][1000 genomes]
rs11760468	1.00[ASN][1000 genomes]
rs11764666	0.82[ASN][1000 genomes]
rs11768749	0.93[ASN][1000 genomes]
rs34623646	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35719886	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59100979	1.00[ASN][1000 genomes]
rs59116230	0.94[EUR][1000 genomes]
rs59568570	0.93[ASN][1000 genomes]
rs60693082	0.83[EUR][1000 genomes]
rs6463541	0.93[ASN][1000 genomes]
rs6463542	0.93[ASN][1000 genomes]
rs6463543	0.93[ASN][1000 genomes]
rs6463544	0.93[ASN][1000 genomes]
rs6955065	0.82[ASN][1000 genomes]
rs6961095	0.82[ASN][1000 genomes]
rs6976305	0.93[ASN][1000 genomes]
rs7780269	0.93[ASN][1000 genomes]
rs7811702	0.93[ASN][1000 genomes]
rs9986688	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv530989	chr7:6176729-6438197	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv482829	chr7:6231809-6407606	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1032987	chr7:6246313-6373054	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv538714	chr7:6246313-6373054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv538715	chr7:6308902-6359025	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1020251	chr7:6309528-6379941	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58052451	PSCD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6319200-6326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:6321000-6326200	Enhancers	Placenta	Placenta
3	chr7:6323800-6325400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr7:6324000-6326000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:6324400-6326000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:6324400-6326000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:6324400-6326000	Weak transcription	NHDF-Ad	bronchial
8	chr7:6324400-6326000	Weak transcription	NHLF	lung
9	chr7:6324400-6329800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:6324400-6334400	Weak transcription	HSMMtube	muscle
11	chr7:6324400-6334400	Weak transcription	Osteobl	bone
12	chr7:6324600-6329600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:6324600-6329600	Weak transcription	HMEC	breast
14	chr7:6324800-6325800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr7:6324800-6326200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:6324800-6329800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:6324800-6329800	Weak transcription	NHEK	skin
18	chr7:6325000-6326000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:6325000-6326000	Weak transcription	A549	lung
20	chr7:6325000-6329600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:6325000-6329600	Weak transcription	Lung	lung
22	chr7:6325000-6329800	Weak transcription	K562	blood

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