Variant report

Variant	rs7258597
Chromosome Location	chr19:38396395-38396396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr19:38396323-38398939	A549	lung:	n/a	chr19:38397652-38397661 chr19:38397845-38397854 chr19:38397847-38397856 chr19:38397843-38397857
2	RAD21	chr19:38396375-38398813	A549	lung:	n/a	chr19:38397076-38397090 chr19:38397691-38397704
3	REST	chr19:38396296-38398563	H1-neurons	neurons:	n/a	n/a
4	MYC	chr19:38396178-38398283	NB4	blood:	n/a	chr19:38398162-38398171 chr19:38397081-38397090 chr19:38397082-38397089
5	MAX	chr19:38396216-38399888	A549	lung:	n/a	chr19:38398162-38398171 chr19:38399338-38399348 chr19:38397081-38397090 chr19:38397082-38397089
6	BCL3	chr19:38396275-38399254	A549	lung:	n/a	chr19:38398115-38398128 chr19:38398114-38398127 chr19:38398116-38398125 chr19:38398111-38398124 chr19:38397977-38397990 chr19:38398005-38398018 chr19:38398113-38398122

No.	Distal block	Cell Line	Cell type
1	chr19:38387761..38390868-chr19:38391934..38396797,4	MCF-7	breast:
2	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
3	chr19:38395958..38396771-chr19:38564609..38565146,2	MCF-7	breast:
4	chr19:38396344..38398889-chr19:38454374..38457525,4	MCF-7	breast:
5	chr19:38395169..38397247-chr19:38624006..38625542,2	MCF-7	breast:
6	chr19:38395370..38399266-chr19:38452571..38456602,5	MCF-7	breast:
7	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
SIPA1L3	TF binding region
ENSG00000105738	Chromatin interaction
ENSG00000268051	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10401637	0.86[EUR][1000 genomes]
rs10401968	0.81[EUR][1000 genomes]
rs10402530	0.82[EUR][1000 genomes]
rs10404567	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10409402	0.80[EUR][1000 genomes]
rs10409487	0.80[EUR][1000 genomes]
rs10420891	0.82[EUR][1000 genomes]
rs10427125	0.82[EUR][1000 genomes]
rs11878269	0.81[EUR][1000 genomes]
rs11879180	0.82[EUR][1000 genomes]
rs12975057	0.82[EUR][1000 genomes]
rs1643462	0.85[EUR][1000 genomes]
rs1643463	0.85[EUR][1000 genomes]
rs1643466	0.85[EUR][1000 genomes]
rs1643467	0.85[EUR][1000 genomes]
rs1643468	0.85[EUR][1000 genomes]
rs1643469	0.87[EUR][1000 genomes]
rs1725477	0.85[EUR][1000 genomes]
rs1725478	0.85[EUR][1000 genomes]
rs1725480	0.85[EUR][1000 genomes]
rs1725481	0.85[EUR][1000 genomes]
rs1725482	0.85[EUR][1000 genomes]
rs1725483	0.85[EUR][1000 genomes]
rs1725485	0.85[EUR][1000 genomes]
rs1725487	0.85[EUR][1000 genomes]
rs1725488	0.83[EUR][1000 genomes]
rs1725494	0.86[EUR][1000 genomes]
rs2075281	0.81[EUR][1000 genomes]
rs2544718	0.86[EUR][1000 genomes]
rs35209753	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353398	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353399	0.89[EUR][1000 genomes]
rs353400	0.89[EUR][1000 genomes]
rs353402	0.89[EUR][1000 genomes]
rs353403	0.87[EUR][1000 genomes]
rs353404	0.89[EUR][1000 genomes]
rs353407	0.89[EUR][1000 genomes]
rs353414	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353415	0.86[EUR][1000 genomes]
rs353416	0.89[EUR][1000 genomes]
rs353417	0.89[EUR][1000 genomes]
rs353419	0.89[EUR][1000 genomes]
rs353420	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353421	0.89[EUR][1000 genomes]
rs353423	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353424	0.89[EUR][1000 genomes]
rs353425	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs353426	0.87[EUR][1000 genomes]
rs353427	0.89[EUR][1000 genomes]
rs353428	0.85[EUR][1000 genomes]
rs353429	0.82[EUR][1000 genomes]
rs353430	0.86[EUR][1000 genomes]
rs3848626	0.81[EUR][1000 genomes]
rs4802135	0.84[EUR][1000 genomes]
rs4803509	0.81[EUR][1000 genomes]
rs4803524	0.82[EUR][1000 genomes]
rs58449039	0.82[EUR][1000 genomes]
rs705492	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs705494	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705500	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7250409	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7250571	0.86[EUR][1000 genomes]
rs7250868	0.86[EUR][1000 genomes]
rs7252010	0.85[EUR][1000 genomes]
rs7257125	0.81[EUR][1000 genomes]
rs752878	0.85[EUR][1000 genomes]
rs8101752	0.81[EUR][1000 genomes]
rs8101858	0.83[EUR][1000 genomes]
rs8102579	0.82[EUR][1000 genomes]
rs8104076	0.81[EUR][1000 genomes]
rs8107341	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110284	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8182498	0.82[EUR][1000 genomes]
rs833895	0.82[EUR][1000 genomes]
rs833896	0.84[EUR][1000 genomes]
rs833897	0.85[EUR][1000 genomes]
rs833898	0.85[EUR][1000 genomes]
rs833926	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304572	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7258597	ZNF571	cis	multi-tissue	Pritchard
rs7258597	WDR87	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38389600-38396600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr19:38392400-38396600	Weak transcription	Placenta	Placenta
3	chr19:38392600-38396600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr19:38394000-38396400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:38394000-38396400	Weak transcription	Fetal Intestine Large	intestine
6	chr19:38394000-38396400	Weak transcription	Fetal Intestine Small	intestine
7	chr19:38394000-38396400	Weak transcription	A549	lung
8	chr19:38394600-38396400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:38396200-38396400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr19:38396200-38396400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr19:38396200-38396400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr19:38396200-38396400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr19:38396200-38396400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr19:38396200-38396400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr19:38396200-38396400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr19:38396200-38396400	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr19:38396200-38396400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:38396200-38396600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:38396200-38396600	Enhancers	Primary B cells from cord blood	blood
20	chr19:38396200-38396600	Enhancers	Primary B cells from peripheral blood	blood
21	chr19:38396200-38396800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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