Variant report

Variant	rs12001678
Chromosome Location	chr9:94520160-94520161
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	chr9:94512038..94515979-chr9:94518272..94520264,3	K562	blood:
2	chr9:94516080..94518691-chr9:94519626..94521518,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10512214	1.00[AMR][1000 genomes]
rs12001172	0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12003706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12003887	1.00[EUR][1000 genomes]
rs12344153	1.00[EUR][1000 genomes]
rs12685556	1.00[AMR][1000 genomes]
rs1406203	1.00[EUR][1000 genomes]
rs16907602	1.00[AMR][1000 genomes]
rs35764413	1.00[AMR][1000 genomes]
rs4295719	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs56091954	1.00[AMR][1000 genomes]
rs56227711	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56239253	1.00[EUR][1000 genomes]
rs59365117	1.00[AMR][1000 genomes]
rs60009660	1.00[AMR][1000 genomes]
rs60217100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60341050	1.00[AMR][1000 genomes]
rs61094317	1.00[AMR][1000 genomes]
rs6479372	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479373	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73513032	1.00[AMR][1000 genomes]
rs73513043	1.00[AMR][1000 genomes]
rs73513061	1.00[AMR][1000 genomes]
rs73513068	1.00[AMR][1000 genomes]
rs73515039	1.00[AMR][1000 genomes]
rs73521420	1.00[AMR][1000 genomes]
rs73521430	1.00[AMR][1000 genomes]
rs7863502	0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7873653	0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv6612	chr9:94490644-94535738	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 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	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
2	chr9:94486200-94521000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:94487000-94535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:94490400-94521000	Weak transcription	Right Atrium	heart
5	chr9:94499800-94520400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:94499800-94522800	Weak transcription	Gastric	stomach
7	chr9:94499800-94523200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:94506200-94523600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:94509800-94521400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:94513400-94520400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:94513400-94521000	Weak transcription	Spleen	Spleen
12	chr9:94514600-94523600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr9:94514800-94527800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:94515800-94522200	Strong transcription	Fetal Stomach	stomach
15	chr9:94516000-94520200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:94517200-94520800	Weak transcription	Fetal Heart	heart
17	chr9:94517800-94521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:94518000-94522200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:94518400-94520800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:94518600-94520800	Weak transcription	K562	blood
21	chr9:94518800-94520200	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:94518800-94520200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:94518800-94521000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:94519000-94520800	Weak transcription	Ovary	ovary
25	chr9:94519000-94521000	Weak transcription	Fetal Lung	lung
26	chr9:94519000-94521400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:94519000-94522000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:94519000-94523000	Weak transcription	Fetal Intestine Large	intestine
29	chr9:94519400-94520400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:94519400-94532400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:94519800-94520800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:94519800-94520800	Weak transcription	Fetal Intestine Small	intestine
33	chr9:94519800-94521000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:94520000-94520800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:94520000-94521200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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