Variant report

Variant	rs6680780
Chromosome Location	chr1:227037742-227037743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799367	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916057	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916059	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580744	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588886	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119853	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12123818	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12125811	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12127440	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12130732	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12138310	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12143886	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12403248	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12405779	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12733650	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12747261	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12760155	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16846644	0.96[EUR][1000 genomes]
rs1800672	0.98[EUR][1000 genomes]
rs1800673	0.98[EUR][1000 genomes]
rs1800681	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2236912	0.94[EUR][1000 genomes]
rs3213436	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34081886	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029375	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35213802	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35244407	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35396772	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35519961	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35744376	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3820649	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3829979	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6426554	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6676065	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6676067	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71648404	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs732479	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7512804	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv3450745	chr1:227035195-227044100	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227026800-227043800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227035000-227039800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:227037200-227037800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:227037200-227038600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:227037200-227043600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:227037400-227038600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:227037600-227039000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:227037600-227039200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:227037600-227043800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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