Variant report

Variant	rs2567724
Chromosome Location	chr9:116921933-116921934
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	chr9:116915372..116918710-chr9:116920861..116924845,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196739	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1431821	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[ASN][1000 genomes]
rs1560538	0.94[ASN][1000 genomes]
rs1864723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1864724	0.86[ASN][1000 genomes]
rs2043196	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2567706	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2567722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2808770	0.94[ASN][1000 genomes]
rs2808771	0.94[ASN][1000 genomes]
rs2808774	0.94[ASN][1000 genomes]
rs2808775	0.94[ASN][1000 genomes]
rs2808776	0.85[CHB][hapmap]
rs2808778	0.86[CHB][hapmap]
rs2808779	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs2808780	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs2808784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2808785	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2808790	0.95[ASN][1000 genomes]
rs2808795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2808796	0.86[ASN][1000 genomes]
rs2808797	0.86[ASN][1000 genomes]
rs4481685	0.90[ASN][1000 genomes]
rs57113194	0.84[ASN][1000 genomes]
rs891722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs891727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv893752	chr9:116899258-116944333	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466526	chr9:116901926-116924781	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv615226	chr9:116901926-116924781	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv615227	chr9:116904534-116924781	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv466527	chr9:116907448-116933449	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv615228	chr9:116907448-116933449	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv466529	chr9:116907553-116930194	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv615229	chr9:116907553-116930194	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv466530	chr9:116916931-116935660	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv615230	chr9:116916931-116935660	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv466531	chr9:116916931-116940418	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv615231	chr9:116916931-116940418	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2567724	HDHD3	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919000-116922400	Enhancers	Stomach Mucosa	stomach
2	chr9:116919000-116925800	Weak transcription	Gastric	stomach
3	chr9:116919000-116936600	Weak transcription	Brain Hippocampus Middle	brain
4	chr9:116919000-116937600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:116919400-116922600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:116919400-116925800	Weak transcription	Ovary	ovary
8	chr9:116919400-116930000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:116919600-116922200	Genic enhancers	Fetal Stomach	stomach
10	chr9:116919600-116922400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:116919600-116923800	Enhancers	Fetal Muscle Leg	muscle
12	chr9:116919600-116924600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:116919600-116925000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:116919600-116925000	Weak transcription	HSMM	muscle
15	chr9:116919600-116925600	Weak transcription	Fetal Heart	heart
16	chr9:116919600-116939600	Weak transcription	Hela-S3	cervix
17	chr9:116919800-116924400	Weak transcription	Right Atrium	heart
18	chr9:116919800-116925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:116919800-116925600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:116919800-116925600	Enhancers	Fetal Intestine Large	intestine
21	chr9:116919800-116925600	Weak transcription	Fetal Kidney	kidney
22	chr9:116919800-116925800	Weak transcription	Lung	lung
23	chr9:116919800-116927000	Enhancers	Liver	Liver
24	chr9:116919800-116927200	Genic enhancers	Fetal Intestine Small	intestine
25	chr9:116920000-116924200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:116920000-116924800	Weak transcription	NHDF-Ad	bronchial
27	chr9:116920200-116923000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:116920400-116922200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:116920400-116925000	Weak transcription	NHLF	lung
30	chr9:116920400-116925600	Weak transcription	HMEC	breast
31	chr9:116920600-116922000	Weak transcription	Esophagus	oesophagus
32	chr9:116920600-116922200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:116920600-116922400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:116920600-116924000	Weak transcription	Pancreas	Pancrea
35	chr9:116920600-116925600	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:116920600-116925600	Weak transcription	Right Ventricle	heart
37	chr9:116920800-116922000	Strong transcription	NHEK	skin
38	chr9:116920800-116923400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:116920800-116925200	Weak transcription	NH-A	brain
40	chr9:116920800-116925600	Weak transcription	HUVEC	blood vessel
41	chr9:116920800-116925800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:116921000-116922200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:116921000-116922200	Enhancers	Stomach Smooth Muscle	stomach
44	chr9:116921000-116922400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr9:116921000-116922400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:116921000-116923000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:116921000-116924400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:116921200-116922400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:116921200-116922400	Enhancers	Duodenum Mucosa	Duodenum
50	chr9:116921200-116923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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