Variant report

Variant	rs41302758
Chromosome Location	chr1:62678009-62678010
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	MAX	chr1:62677580-62678411	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:62677525-62680163	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:62677510-62680500	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:62677987-62678442	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD2	chr1:62675567-62679535	H1-hESC	embryonic stem cell:	n/a	n/a
6	GTF2F1	chr1:62675517-62679496	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr1:62677938-62678200	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr1:62677544-62678395	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:62671110-62680443	H1-hESC	embryonic stem cell:	n/a	n/a
10	SP4	chr1:62677503-62678717	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAFK	chr1:62677786-62678437	H1-hESC	embryonic stem cell:	n/a	n/a
12	ATF2	chr1:62677516-62679529	H1-hESC	embryonic stem cell:	n/a	n/a
13	TAF7	chr1:62677524-62678573	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:62672294-62680406	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000237227	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11802059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122679	0.97[ASN][1000 genomes]
rs12130050	0.97[ASN][1000 genomes]
rs12137401	0.95[ASN][1000 genomes]
rs41296165	0.81[AFR][1000 genomes]
rs41306639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41306641	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41312734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41313367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915801	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4915802	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210125	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66958136	0.95[ASN][1000 genomes]
rs67334216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67788504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72921870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7367812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7367828	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv870842	chr1:62644118-62679202	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62666000-62695400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:62671800-62678200	Strong transcription	H1 Cell Line	embryonic stem cell
3	chr1:62674400-62678800	Weak transcription	Colonic Mucosa	Colon
4	chr1:62675800-62684600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:62676200-62680400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:62676200-62683400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62676200-62683600	Weak transcription	Right Atrium	heart
8	chr1:62676200-62689600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:62677000-62680600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:62677200-62678200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:62677200-62680600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:62677200-62682600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:62677200-62689400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62677200-62693400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:62677200-62694000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:62677200-62694000	Weak transcription	Fetal Lung	lung
17	chr1:62677400-62683000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:62677400-62683200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:62677600-62689200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:62677800-62683400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:62677800-62683600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:62678000-62683000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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