Variant report

Variant	rs2790390
Chromosome Location	chr9:97361995-97361996
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	chr9:97360979..97363553-chr9:97393005..97395544,2	MCF-7	breast:
2	chr9:97333743..97336722-chr9:97359939..97362910,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1042144	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821376	0.84[EUR][1000 genomes]
rs10993275	0.83[EUR][1000 genomes]
rs10993277	0.84[EUR][1000 genomes]
rs10993278	0.83[EUR][1000 genomes]
rs12238876	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13284668	0.88[EUR][1000 genomes]
rs13291835	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13296485	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16937175	0.86[EUR][1000 genomes]
rs1754435	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1754439	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296708	0.88[EUR][1000 genomes]
rs2460138	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2679599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2679602	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2772022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369670	0.85[EUR][1000 genomes]
rs2945802	0.91[AFR][1000 genomes]
rs2987882	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2987897	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2993905	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2993912	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2993958	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2993959	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2993961	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2993962	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3896183	0.84[EUR][1000 genomes]
rs4075984	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743961	0.88[EUR][1000 genomes]
rs4744362	0.88[EUR][1000 genomes]
rs479197	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs514222	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs515339	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs518768	0.91[AFR][1000 genomes]
rs540124	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs543731	0.91[AFR][1000 genomes]
rs547834	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548348	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576745	0.94[EUR][1000 genomes]
rs583365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590090	0.82[AFR][1000 genomes]
rs632506	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs652867	0.84[AFR][1000 genomes]
rs67721291	0.88[EUR][1000 genomes]
rs688843	0.91[AFR][1000 genomes]
rs693399	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs781650	0.91[AFR][1000 genomes]
rs802918	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs8192689	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs874248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
4	nsv466436	chr9:97343620-97369149	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv614917	chr9:97343620-97369149	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97347600-97374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97351800-97369200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97356400-97365600	Weak transcription	Psoas Muscle	Psoas
4	chr9:97356600-97362400	Weak transcription	Fetal Intestine Small	intestine
5	chr9:97357000-97362000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:97357000-97362400	Weak transcription	Stomach Mucosa	stomach
7	chr9:97358000-97368800	Weak transcription	Gastric	stomach
8	chr9:97360600-97362400	Enhancers	HepG2	liver
9	chr9:97361200-97362800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr9:97361800-97362000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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