Variant report

Variant	rs28402401
Chromosome Location	chr9:97395041-97395042
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97373691..97376847-chr9:97393054..97396710,3	MCF-7	breast:
2	chr9:97389746..97395320-chr9:97854192..97858136,7	MCF-7	breast:
3	chr9:97360979..97363553-chr9:97393005..97395544,2	MCF-7	breast:
4	chr9:97393707..97398253-chr9:97766180..97769017,4	MCF-7	breast:
5	chr9:97393391..97395196-chr9:97892426..97894999,2	MCF-7	breast:
6	chr9:97392176..97395070-chr9:97431603..97433493,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12683407	0.85[EUR][1000 genomes]
rs12684841	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12684849	0.85[EUR][1000 genomes]
rs12685485	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16910850	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16910853	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16910860	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296707	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28369691	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28369738	0.85[EUR][1000 genomes]
rs28369782	0.85[EUR][1000 genomes]
rs28369786	0.85[EUR][1000 genomes]
rs28402377	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402378	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402384	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402386	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402389	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402390	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28402396	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402397	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402404	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4111369	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4574908	0.87[EUR][1000 genomes]
rs59327242	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59727084	0.85[EUR][1000 genomes]
rs7019207	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028990	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035325	0.84[ASN][1000 genomes]
rs73523269	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73523271	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849320	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850385	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7859022	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859489	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867069	0.85[EUR][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	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	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
3	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97371400-97401000	Weak transcription	Spleen	Spleen
2	chr9:97381400-97400400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:97381600-97401000	Weak transcription	Right Atrium	heart
4	chr9:97382800-97399400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr9:97390000-97397600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:97391800-97395400	Enhancers	Pancreas	Pancrea
7	chr9:97391800-97396000	Enhancers	Fetal Intestine Large	intestine
8	chr9:97392000-97395400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:97392600-97395200	Enhancers	Colonic Mucosa	Colon
10	chr9:97392600-97395200	Enhancers	NHEK	skin
11	chr9:97392800-97395200	Enhancers	Fetal Lung	lung
12	chr9:97392800-97395200	Enhancers	Lung	lung
13	chr9:97392800-97395600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:97393200-97395800	Enhancers	Fetal Stomach	stomach
15	chr9:97394000-97395200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:97394000-97395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:97394000-97395200	Enhancers	Fetal Intestine Small	intestine
18	chr9:97394000-97395200	Weak transcription	Gastric	stomach
19	chr9:97394000-97400600	Weak transcription	Small Intestine	intestine
20	chr9:97394200-97395200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:97394200-97395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:97394200-97400800	Weak transcription	Adipose Nuclei	Adipose
23	chr9:97394400-97395800	Enhancers	Duodenum Mucosa	Duodenum
24	chr9:97394600-97395200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:97394600-97395600	Enhancers	Stomach Mucosa	stomach
26	chr9:97395000-97395200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr9:97395000-97395400	Enhancers	Brain Anterior Caudate	brain
28	chr9:97395000-97395400	Enhancers	Brain Substantia Nigra	brain
29	chr9:97395000-97395800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:97395000-97395800	Enhancers	Brain Germinal Matrix	brain
31	chr9:97395000-97397400	Enhancers	Liver	Liver

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