Variant report

Variant	rs12002297
Chromosome Location	chr9:16559255-16559256
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10117448	0.86[ASN][1000 genomes]
rs10121959	0.86[ASN][1000 genomes]
rs10511622	0.86[ASN][1000 genomes]
rs10962492	0.86[ASN][1000 genomes]
rs10962493	0.86[ASN][1000 genomes]
rs12000225	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12000228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002673	0.86[ASN][1000 genomes]
rs12004947	0.86[ASN][1000 genomes]
rs12338548	1.00[ASN][1000 genomes]
rs12343239	0.86[ASN][1000 genomes]
rs12343306	0.86[ASN][1000 genomes]
rs16934806	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927616	1.00[ASN][1000 genomes]
rs1927617	0.86[ASN][1000 genomes]
rs1952345	1.00[ASN][1000 genomes]
rs2065937	0.86[ASN][1000 genomes]
rs28414647	1.00[ASN][1000 genomes]
rs28483319	1.00[ASN][1000 genomes]
rs28593297	1.00[ASN][1000 genomes]
rs28602416	1.00[ASN][1000 genomes]
rs28714603	1.00[ASN][1000 genomes]
rs6475060	1.00[ASN][1000 genomes]
rs6475062	1.00[ASN][1000 genomes]
rs6475063	0.86[ASN][1000 genomes]
rs7018594	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021199	1.00[ASN][1000 genomes]
rs7029578	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029648	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7035791	1.00[ASN][1000 genomes]
rs73417482	0.83[AFR][1000 genomes]
rs73417483	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73419403	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847768	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857751	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858025	1.00[ASN][1000 genomes]
rs7861969	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863885	0.86[ASN][1000 genomes]
rs7870380	1.00[ASN][1000 genomes]
rs943748	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][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	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16542600-16564000	Weak transcription	HUVEC	blood vessel
2	chr9:16543800-16567000	Weak transcription	HSMMtube	muscle
3	chr9:16544000-16559600	Weak transcription	Small Intestine	intestine
4	chr9:16546000-16559600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:16546000-16559800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:16546000-16568400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:16550800-16559800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:16551800-16567800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:16552000-16559600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:16552000-16567800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:16552800-16559800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:16552800-16566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:16552800-16570200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:16552800-16571000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:16552800-16571400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:16553000-16559600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:16553000-16570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:16553000-16575200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:16554000-16559600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:16554600-16559800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:16554800-16561200	Weak transcription	Osteobl	bone
22	chr9:16556400-16559400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr9:16556400-16560200	Weak transcription	Colonic Mucosa	Colon
24	chr9:16556400-16566000	Weak transcription	Fetal Stomach	stomach
25	chr9:16556400-16569200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:16556400-16570600	Weak transcription	NHLF	lung
27	chr9:16556400-16575600	Weak transcription	HSMM	muscle
28	chr9:16556600-16561000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:16557200-16559800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr9:16558800-16559600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:16559000-16560400	Enhancers	Colon Smooth Muscle	Colon
32	chr9:16559200-16560200	Enhancers	Ovary	ovary

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