Variant report

Variant	rs7848221
Chromosome Location	chr9:97224777-97224778
allele	C/T
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	chr9:97220678..97222830-chr9:97224349..97226700,3	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12342163	0.86[AFR][1000 genomes]
rs2006685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049008	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277182	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2986859	0.84[ASN][1000 genomes]
rs2987115	0.83[ASN][1000 genomes]
rs4434674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4477096	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4497033	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509403	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743953	0.82[ASN][1000 genomes]
rs4743954	0.86[ASN][1000 genomes]
rs4743955	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4744346	0.86[ASN][1000 genomes]
rs600442	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6479544	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs684892	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7020879	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7023744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7023915	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7024159	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7025755	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7027465	0.84[ASN][1000 genomes]
rs7027489	0.80[ASN][1000 genomes]
rs7031088	0.84[ASN][1000 genomes]
rs7031496	0.86[ASN][1000 genomes]
rs7031949	0.84[ASN][1000 genomes]
rs7037190	0.84[ASN][1000 genomes]
rs7037198	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040577	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7040710	0.84[ASN][1000 genomes]
rs7047279	0.89[ASN][1000 genomes]
rs7047295	0.87[ASN][1000 genomes]
rs7047930	0.86[ASN][1000 genomes]
rs7048688	0.84[ASN][1000 genomes]
rs7848227	0.86[ASN][1000 genomes]
rs7853182	0.81[ASN][1000 genomes]
rs7860616	0.86[ASN][1000 genomes]
rs7863310	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863312	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868562	0.85[ASN][1000 genomes]
rs9299421	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9299422	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9409552	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409759	0.86[ASN][1000 genomes]
rs9409763	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9409777	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409779	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9777207	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	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
6	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
7	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7848221	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97201000-97225000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr9:97201000-97225800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr9:97201400-97225200	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:97201600-97224800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:97202200-97225600	Strong transcription	Dnd41	blood
6	chr9:97203200-97225000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:97204400-97227000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:97206200-97225800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:97206800-97225200	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr9:97206800-97225600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:97207000-97225800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr9:97207200-97224800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:97208200-97224800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:97208400-97225200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr9:97209000-97225000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr9:97209000-97225400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:97209200-97225200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr9:97209200-97225600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr9:97209600-97224800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:97209800-97225200	Strong transcription	Placenta	Placenta
21	chr9:97209800-97225600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:97210000-97225200	Strong transcription	Fetal Muscle Leg	muscle
23	chr9:97212400-97224800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:97212600-97225400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:97212600-97225400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr9:97213800-97224800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr9:97215200-97225400	Strong transcription	Primary B cells from cord blood	blood
28	chr9:97215200-97225400	Strong transcription	Primary T cells from cord blood	blood
29	chr9:97215200-97225800	Strong transcription	HSMM	muscle
30	chr9:97215400-97225200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:97215400-97225400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:97215800-97225000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:97215800-97225000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr9:97215800-97225200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:97215800-97225200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr9:97215800-97225400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:97215800-97225600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr9:97215800-97225600	Strong transcription	Ovary	ovary
39	chr9:97216000-97225400	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:97216000-97225600	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:97216200-97225200	Strong transcription	HMEC	breast
42	chr9:97216400-97226000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:97217000-97226600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr9:97217600-97225200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr9:97217800-97225600	Strong transcription	Fetal Intestine Large	intestine
46	chr9:97218200-97225800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:97218800-97225200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr9:97218800-97225600	Weak transcription	Fetal Heart	heart
49	chr9:97219600-97225200	Strong transcription	HUVEC	blood vessel
50	chr9:97219800-97225000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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