Variant report

Variant	rs16842326
Chromosome Location	chr1:224047647-224047648
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	chr1:224047358-224048344	T-47D	breast:	n/a	chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047812-224047824 chr1:224047743-224047753 chr1:224047739-224047760
2	GATA2	chr1:224047637-224048146	SH-SY5Y	brain:	n/a	chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047812-224047824 chr1:224047743-224047753 chr1:224047739-224047760
3	GATA3	chr1:224047492-224048512	MCF-7	breast:	n/a	chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047812-224047824 chr1:224047743-224047753 chr1:224047739-224047760
4	GATA3	chr1:224047603-224048347	T-47D	breast:	n/a	chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047812-224047824 chr1:224047743-224047753 chr1:224047739-224047760
5	SIN3AK20	chr1:224047630-224048603	MCF-7	breast:	n/a	n/a
6	GATA3	chr1:224047511-224048513	MCF-7	breast:	n/a	chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047746-224047753 chr1:224047812-224047824 chr1:224047743-224047753 chr1:224047739-224047760

No.	Distal block	Cell Line	Cell type
1	chr1:224043695..224046031-chr1:224047315..224049831,3	K562	blood:
2	chr1:224030773..224035996-chr1:224045738..224052159,10	MCF-7	breast:
3	chr1:224042155..224044743-chr1:224047523..224049219,2	MCF-7	breast:
4	chr1:224032237..224035602-chr1:224046110..224051630,7	MCF-7	breast:

Variant related genes	Relation type
PHBP11	TF binding region
ENSG00000227621	Chromatin interaction
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10495215	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10495216	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10495217	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10503144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153965	0.83[EUR][1000 genomes]
rs12046297	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12059128	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060361	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066704	0.85[CEU][hapmap]
rs12069561	0.85[CEU][hapmap]
rs12080250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12091841	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222138	0.85[CEU][hapmap]
rs1222141	0.85[CEU][hapmap]
rs12563477	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12564557	1.00[ASN][1000 genomes]
rs12565202	1.00[ASN][1000 genomes]
rs12565573	1.00[ASN][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568612	0.85[CEU][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16842162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842343	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17556570	0.85[CEU][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17557525	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17557623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17598	0.85[CEU][hapmap]
rs28370073	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28370074	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28370088	0.84[EUR][1000 genomes]
rs28370159	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370170	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683843	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032024	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738373	0.85[CEU][hapmap]
rs3738374	0.85[CEU][hapmap]
rs3885657	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303996	1.00[ASN][1000 genomes]
rs4653522	0.85[CEU][hapmap]
rs58774026	1.00[ASN][1000 genomes]
rs61823580	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61823581	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.88[EUR][1000 genomes]
rs61824008	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604727	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604729	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671245	1.00[CEU][hapmap]
rs6678365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683052	1.00[CEU][hapmap]
rs6685475	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6685557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693372	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693884	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6694960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703104	0.85[CEU][hapmap]
rs73116425	1.00[ASN][1000 genomes]
rs73116447	1.00[ASN][1000 genomes]
rs73116451	1.00[ASN][1000 genomes]
rs73116456	1.00[ASN][1000 genomes]
rs7331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs751609	0.85[CEU][hapmap]
rs7528455	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549063	1.00[CEU][hapmap];1.00[JPT][hapmap]

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	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224044800-224047800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:224044800-224051800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:224046000-224048600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224046800-224048400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:224047000-224048600	Enhancers	NHEK	skin
6	chr1:224047200-224048400	Enhancers	Hela-S3	cervix
7	chr1:224047200-224048600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:224047200-224048600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:224047400-224048200	Enhancers	Brain Substantia Nigra	brain
10	chr1:224047400-224048600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:224047600-224048000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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