Variant report

Variant	rs9299421
Chromosome Location	chr9:97215617-97215618
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97214734..97217712-chr9:97223589..97225379,2	MCF-7	breast:
2	chr9:97206178..97208805-chr9:97213845..97216691,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs2006685	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049008	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277182	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4434674	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4477096	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4497033	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4509403	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743953	0.88[ASN][1000 genomes]
rs4743954	0.92[ASN][1000 genomes]
rs4743955	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744340	0.83[ASN][1000 genomes]
rs4744346	0.94[ASN][1000 genomes]
rs600442	0.83[EUR][1000 genomes]
rs6479544	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs684892	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs688165	0.85[ASN][1000 genomes]
rs7020879	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7023744	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7023915	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7024159	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7025755	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7027465	0.92[ASN][1000 genomes]
rs7027489	0.88[ASN][1000 genomes]
rs7031088	0.90[ASN][1000 genomes]
rs7031496	0.94[ASN][1000 genomes]
rs7031949	0.89[ASN][1000 genomes]
rs7037190	0.89[ASN][1000 genomes]
rs7037198	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7038593	0.82[ASN][1000 genomes]
rs7040577	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7040710	0.92[ASN][1000 genomes]
rs7047279	0.95[ASN][1000 genomes]
rs7047295	0.92[ASN][1000 genomes]
rs7047930	0.92[ASN][1000 genomes]
rs7048688	0.89[ASN][1000 genomes]
rs7848221	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7848227	0.94[ASN][1000 genomes]
rs7863310	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7863312	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7868562	0.90[ASN][1000 genomes]
rs7873525	0.84[ASN][1000 genomes]
rs9299422	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409552	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409759	0.94[ASN][1000 genomes]
rs9409763	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9409765	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9409777	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9409779	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9777207	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	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
5	esv33917	chr9:97185592-97216212	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv893593	chr9:97196979-97228918	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9299421	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
2	chr9:97181400-97215800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:97190400-97215800	Weak transcription	Ovary	ovary
4	chr9:97192200-97221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:97193800-97216000	Weak transcription	Brain Substantia Nigra	brain
6	chr9:97194000-97216000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:97195200-97216000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:97195200-97216000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:97195600-97218000	Weak transcription	Pancreas	Pancrea
10	chr9:97199400-97221400	Weak transcription	Psoas Muscle	Psoas
11	chr9:97201000-97223400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:97201000-97224600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:97201400-97221400	Weak transcription	Stomach Mucosa	stomach
16	chr9:97201400-97225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr9:97201600-97224800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:97202000-97224200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr9:97202200-97215800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:97202200-97216000	Weak transcription	Brain Angular Gyrus	brain
21	chr9:97202200-97225600	Strong transcription	Dnd41	blood
22	chr9:97202400-97222600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:97203000-97215800	Weak transcription	Brain Anterior Caudate	brain
24	chr9:97203200-97225000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:97203800-97217000	Weak transcription	HepG2	liver
26	chr9:97204000-97215800	Weak transcription	Small Intestine	intestine
27	chr9:97204000-97215800	Weak transcription	NHLF	lung
28	chr9:97204200-97222800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:97204400-97227000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:97204600-97216200	Weak transcription	Fetal Brain Male	brain
31	chr9:97204800-97216000	Weak transcription	Spleen	Spleen
32	chr9:97206200-97225800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:97206600-97224400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:97206800-97225200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr9:97206800-97225600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:97207000-97225800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr9:97207200-97216000	Weak transcription	Gastric	stomach
38	chr9:97207200-97218000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:97207200-97224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:97207400-97215800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:97207400-97216000	Weak transcription	Left Ventricle	heart
42	chr9:97207400-97218000	Weak transcription	Esophagus	oesophagus
43	chr9:97208000-97215800	Weak transcription	Right Ventricle	heart
44	chr9:97208200-97224800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:97208400-97221400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:97208400-97222800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:97208400-97224600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:97208400-97225200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr9:97208600-97216200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:97208600-97217800	Weak transcription	Fetal Heart	heart

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