Variant report

Variant	rs4564741
Chromosome Location	chr2:189271456-189271457
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	chr2:189252210..189254786-chr2:189270636..189272826,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10185828	0.80[ASN][1000 genomes]
rs10192374	0.84[ASN][1000 genomes]
rs10204674	0.84[ASN][1000 genomes]
rs10209733	0.80[ASN][1000 genomes]
rs10804020	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931346	0.81[EUR][1000 genomes]
rs10931356	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931359	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11682085	0.82[ASN][1000 genomes]
rs12465164	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12465625	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12469904	0.83[EUR][1000 genomes]
rs12473653	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12473872	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12474692	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12611919	0.89[EUR][1000 genomes]
rs12613615	0.82[ASN][1000 genomes]
rs12624002	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13008931	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13014693	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13022513	0.83[EUR][1000 genomes]
rs13415123	0.80[ASN][1000 genomes]
rs34189381	0.81[ASN][1000 genomes]
rs34445909	0.83[EUR][1000 genomes]
rs34778517	0.85[EUR][1000 genomes]
rs35180255	0.87[EUR][1000 genomes]
rs35365782	0.85[EUR][1000 genomes]
rs35964306	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4340469	0.83[ASN][1000 genomes]
rs4381753	0.81[EUR][1000 genomes]
rs4426503	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4458180	0.80[ASN][1000 genomes]
rs4516391	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4591312	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4599076	0.83[EUR][1000 genomes]
rs4610010	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666759	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667215	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4667221	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667222	0.85[EUR][1000 genomes]
rs58978246	0.80[ASN][1000 genomes]
rs59106803	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183206	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183212	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62183213	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704814	0.81[ASN][1000 genomes]
rs6712056	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6724636	0.83[EUR][1000 genomes]
rs6724867	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6744629	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753371	0.83[EUR][1000 genomes]
rs7425596	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7566619	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574262	0.89[ASN][1000 genomes]
rs7586390	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7593546	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7595377	0.80[ASN][1000 genomes]
rs7598279	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv9852	chr2:189267263-189277181	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4564741	GULP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189251000-189285200	Weak transcription	Aorta	Aorta
2	chr2:189264000-189283800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:189264400-189274200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:189268600-189279800	Weak transcription	NHLF	lung
5	chr2:189270400-189276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:189270600-189271600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:189270600-189272800	Weak transcription	Esophagus	oesophagus
8	chr2:189270600-189281000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:189270600-189285200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:189270600-189285200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:189270800-189276800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:189271000-189272000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:189271000-189273400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:189271000-189275200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:189271000-189278400	Weak transcription	A549	lung
16	chr2:189271000-189285200	Weak transcription	Fetal Lung	lung
17	chr2:189271200-189271600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:189271200-189272400	Weak transcription	H1 Cell Line	embryonic stem cell

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