Variant report

Variant	rs12683746
Chromosome Location	chr9:94567977-94567978
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	chr9:94560147..94563596-chr9:94565851..94569196,3	MCF-7	breast:
2	chr9:94566439..94568761-chr9:94577681..94581250,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10820904	0.82[CEU][hapmap]
rs10992114	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992116	0.82[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10992117	0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12336034	0.90[AMR][1000 genomes]
rs16907798	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103301	0.90[AMR][1000 genomes]
rs35357880	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3802380	0.90[AMR][1000 genomes]
rs4743852	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743854	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744101	0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744102	0.90[AMR][1000 genomes]
rs4744103	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744104	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59394284	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73513266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855006	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855609	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858240	0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs7861514	0.82[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7864140	0.93[YRI][hapmap]
rs7867961	0.82[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7872107	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7872492	0.82[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299398	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	nsv523940	chr9:94546564-94573753	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv518372	chr9:94558126-94605908	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	1 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	chr9:94560800-94568000	Enhancers	Rectal Smooth Muscle	rectum
2	chr9:94562000-94575400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:94562000-94579400	Weak transcription	Gastric	stomach
4	chr9:94564600-94568000	Enhancers	Fetal Stomach	stomach
5	chr9:94565000-94568600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:94565200-94568000	Enhancers	Fetal Muscle Leg	muscle
7	chr9:94565200-94568600	Enhancers	Fetal Heart	heart
8	chr9:94565200-94571800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:94565200-94573000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:94565400-94568800	Enhancers	Colon Smooth Muscle	Colon
11	chr9:94565400-94575200	Enhancers	Stomach Smooth Muscle	stomach
12	chr9:94566400-94568000	Enhancers	Right Atrium	heart
13	chr9:94566600-94568200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:94566600-94568400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:94566600-94569800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:94566600-94571600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:94566600-94571800	Weak transcription	Fetal Intestine Small	intestine
18	chr9:94566800-94569800	Weak transcription	K562	blood
19	chr9:94566800-94571600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:94567000-94571400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:94567000-94571400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:94567000-94571600	Weak transcription	NHDF-Ad	bronchial
23	chr9:94567200-94571600	Weak transcription	Spleen	Spleen
24	chr9:94567400-94569800	Weak transcription	Fetal Lung	lung
25	chr9:94567600-94568200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:94567600-94575400	Weak transcription	Ovary	ovary
27	chr9:94567800-94571600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:94567800-94571600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:94567800-94571600	Weak transcription	Esophagus	oesophagus
30	chr9:94567800-94571800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:94567800-94571800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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