Variant report

Variant	rs12402699
Chromosome Location	chr1:171392009-171392010
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	GATA3	chr1:171391400-171392019	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNU6-290P	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10798394	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798395	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912911	0.85[EUR][1000 genomes]
rs11579231	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12072674	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12121150	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126686	0.98[ASN][1000 genomes]
rs12402708	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207189	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689514	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72637249	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv470745	chr1:171381746-171409514	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv465628	chr1:171381746-171409515	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv548189	chr1:171381746-171409515	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171388800-171394600	Enhancers	NHEK	skin
2	chr1:171389600-171394400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:171389600-171394600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:171390600-171392800	Enhancers	NHLF	lung
5	chr1:171390600-171393600	Enhancers	Placenta	Placenta
6	chr1:171390800-171393000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:171390800-171398200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:171391200-171395600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:171391200-171397400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:171391200-171397800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:171391600-171392200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:171391600-171392200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:171391600-171392200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:171391600-171392200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:171391600-171392200	Enhancers	NH-A	brain
16	chr1:171391600-171392600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:171391800-171392200	Enhancers	HMEC	breast
18	chr1:171391800-171392200	Enhancers	NHDF-Ad	bronchial
19	chr1:171391800-171392400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:171391800-171393600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:171391800-171393600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:171391800-171393800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:171391800-171395200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:171392000-171392800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:171392000-171393800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:171392000-171395400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:171392000-171395600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:171392000-171396800	Weak transcription	HUVEC	blood vessel

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