Variant report

Variant	rs28402404
Chromosome Location	chr9:97394238-97394239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:97375440..97378542-chr9:97391725..97394611,4	MCF-7	breast:
2	chr9:97373691..97376847-chr9:97393054..97396710,3	MCF-7	breast:
3	chr9:97389746..97395320-chr9:97854192..97858136,7	MCF-7	breast:
4	chr9:97360979..97363553-chr9:97393005..97395544,2	MCF-7	breast:
5	chr9:97393707..97398253-chr9:97766180..97769017,4	MCF-7	breast:
6	chr9:97393391..97395196-chr9:97892426..97894999,2	MCF-7	breast:
7	chr9:97325572..97327725-chr9:97393482..97394985,2	MCF-7	breast:
8	chr9:97393231..97394953-chr9:97687496..97690303,2	MCF-7	breast:
9	chr9:97391705..97394418-chr9:97757936..97760772,2	MCF-7	breast:
10	chr9:97392176..97395070-chr9:97431603..97433493,2	MCF-7	breast:

No data

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	0.88[EUR][1000 genomes]
rs12684841	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12684849	0.88[EUR][1000 genomes]
rs12685485	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16910850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16910853	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16910860	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296707	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28369691	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28369738	0.88[EUR][1000 genomes]
rs28369782	0.88[EUR][1000 genomes]
rs28369786	0.88[EUR][1000 genomes]
rs28402377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402378	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402389	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402396	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402397	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28402401	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4111369	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4574908	0.86[EUR][1000 genomes]
rs59327242	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59727084	0.88[EUR][1000 genomes]
rs7019207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7028990	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7035325	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73523269	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73523271	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7849320	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850385	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7859022	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859489	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7867069	0.88[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:35 , 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	chr9:97392400-97395000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:97392600-97394400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:97392600-97394400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr9:97392600-97394600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr9:97392600-97395200	Enhancers	Colonic Mucosa	Colon
14	chr9:97392600-97395200	Enhancers	NHEK	skin
15	chr9:97392800-97394600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr9:97392800-97395200	Enhancers	Fetal Lung	lung
17	chr9:97392800-97395200	Enhancers	Lung	lung
18	chr9:97392800-97395600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:97393000-97394400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr9:97393000-97395000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr9:97393200-97395800	Enhancers	Fetal Stomach	stomach
22	chr9:97393400-97394400	Flanking Active TSS	Liver	Liver
23	chr9:97393600-97395000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:97393800-97394600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:97394000-97394400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr9:97394000-97395200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:97394000-97395200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:97394000-97395200	Enhancers	Fetal Intestine Small	intestine
29	chr9:97394000-97395200	Weak transcription	Gastric	stomach
30	chr9:97394000-97400600	Weak transcription	Small Intestine	intestine
31	chr9:97394200-97394600	Weak transcription	Stomach Mucosa	stomach
32	chr9:97394200-97395000	Bivalent Enhancer	HepG2	liver
33	chr9:97394200-97395200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:97394200-97395200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:97394200-97400800	Weak transcription	Adipose Nuclei	Adipose

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