Variant report

Variant	rs6564172
Chromosome Location	chr16:74846046-74846047
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	chr16:74701971..74704127-chr16:74845160..74847638,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11149767	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11149768	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12716770	0.85[EUR][1000 genomes]
rs28751066	0.93[ASN][1000 genomes]
rs35492657	0.84[ASN][1000 genomes]
rs61477784	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7201427	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8045562	0.86[EUR][1000 genomes]
rs9931212	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer 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 miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1061948	chr16:74660609-74882915	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	nsv542957	chr16:74660609-74882915	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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 miRNA target site	111 gene(s)	inside rSNPs	diseases
7	nsv1058900	chr16:74753819-75005050	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv542958	chr16:74753819-75005050	Weak transcription Bivalent Enhancer Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	esv3345041	chr16:74756263-75066969	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	nsv457520	chr16:74758984-74907440	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv572976	chr16:74758984-74907440	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	esv2761913	chr16:74828988-74876348	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv431516	chr16:74840166-75099566	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6564172	CFDP1	cis	parietal	SCAN
rs6564172	CALB2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74841800-74846800	Weak transcription	Fetal Intestine Small	intestine
2	chr16:74844400-74847200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:74844600-74847600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
4	chr16:74845400-74846200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
5	chr16:74845400-74846200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr16:74845400-74846400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:74845400-74847000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr16:74845600-74846200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr16:74845600-74846200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr16:74845600-74846200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr16:74845600-74846200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr16:74845600-74846800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr16:74845600-74847600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr16:74845800-74846200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
15	chr16:74845800-74846600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr16:74845800-74846600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr16:74846000-74846200	Enhancers	Gastric	stomach
18	chr16:74846000-74846200	Enhancers	Lung	lung
19	chr16:74846000-74846200	Enhancers	Right Atrium	heart
20	chr16:74846000-74846200	Enhancers	A549	lung
21	chr16:74846000-74846400	Enhancers	Esophagus	oesophagus
22	chr16:74846000-74846600	Enhancers	Brain Cingulate Gyrus	brain
23	chr16:74846000-74846600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr16:74846000-74846600	Enhancers	Hela-S3	cervix
25	chr16:74846000-74846800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr16:74846000-74847400	Enhancers	Brain Substantia Nigra	brain
27	chr16:74846000-74847600	Enhancers	Brain Angular Gyrus	brain
28	chr16:74846000-74847600	Enhancers	Brain Hippocampus Middle	brain
29	chr16:74846000-74848000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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