Variant report

Variant	rs9999362
Chromosome Location	chr4:122729505-122729506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:122728633-122729620	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:122727884..122730425-chr4:122743286..122746200,2	MCF-7	breast:

Variant related genes	Relation type
EXOSC9	TF binding region
ENSG00000145386	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10001889	0.97[ASN][1000 genomes]
rs10004284	0.97[ASN][1000 genomes]
rs10007956	0.97[ASN][1000 genomes]
rs10013916	0.97[ASN][1000 genomes]
rs10023020	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10024820	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10084948	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1048433	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098643	0.97[ASN][1000 genomes]
rs11724322	0.97[ASN][1000 genomes]
rs11733882	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11734075	0.94[ASN][1000 genomes]
rs12510839	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13106764	0.97[ASN][1000 genomes]
rs13108419	0.81[ASN][1000 genomes]
rs13119055	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130789	0.90[ASN][1000 genomes]
rs13140070	0.98[ASN][1000 genomes]
rs13145213	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13152701	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17005256	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271176	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28435300	0.98[ASN][1000 genomes]
rs28522256	0.98[ASN][1000 genomes]
rs28672860	0.98[ASN][1000 genomes]
rs3217772	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34445121	0.98[ASN][1000 genomes]
rs35341163	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35495505	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762840	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811742	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833233	0.91[ASN][1000 genomes]
rs4833234	0.94[ASN][1000 genomes]
rs4833235	0.94[ASN][1000 genomes]
rs4833236	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4833773	0.90[ASN][1000 genomes]
rs4833775	0.98[ASN][1000 genomes]
rs5004355	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67150579	0.98[ASN][1000 genomes]
rs67775544	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811867	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6830443	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845901	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs769236	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs966555	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995319	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998785	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers 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 target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9999362	CCNA2	Cis_1M	lymphoblastoid	RTeQTL
rs9999362	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122723000-122729600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:122723000-122733400	Weak transcription	Pancreas	Pancrea
3	chr4:122723000-122743600	Weak transcription	Esophagus	oesophagus
4	chr4:122723000-122743600	Weak transcription	Small Intestine	intestine
5	chr4:122723000-122744200	Weak transcription	Gastric	stomach
6	chr4:122723000-122744600	Weak transcription	Aorta	Aorta
7	chr4:122723200-122731400	Weak transcription	Right Ventricle	heart
8	chr4:122723200-122737000	Weak transcription	Colonic Mucosa	Colon
9	chr4:122723200-122741800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:122723200-122743400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:122723200-122743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:122723200-122743800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:122723400-122744200	Weak transcription	Stomach Mucosa	stomach
14	chr4:122723600-122732400	Weak transcription	Psoas Muscle	Psoas
15	chr4:122723600-122742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:122723600-122742400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:122723600-122742800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:122723800-122733000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:122723800-122734000	Strong transcription	Left Ventricle	heart
20	chr4:122723800-122736400	Strong transcription	Fetal Muscle Leg	muscle
21	chr4:122723800-122739400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:122723800-122739600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr4:122723800-122739600	Strong transcription	Liver	Liver
24	chr4:122723800-122740000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:122723800-122740000	Strong transcription	Osteobl	bone
26	chr4:122723800-122740400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:122723800-122740400	Strong transcription	Fetal Intestine Large	intestine
28	chr4:122723800-122740600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:122723800-122741800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr4:122723800-122742200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:122723800-122742400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:122723800-122743000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr4:122723800-122743000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:122723800-122743000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr4:122724000-122730200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:122724000-122731600	Strong transcription	Brain Anterior Caudate	brain
37	chr4:122724000-122732400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:122724000-122733000	Strong transcription	Fetal Lung	lung
39	chr4:122724000-122735800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:122724000-122738200	Strong transcription	NHDF-Ad	bronchial
41	chr4:122724000-122740000	Strong transcription	Primary B cells from cord blood	blood
42	chr4:122724000-122740200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:122724000-122740400	Strong transcription	Placenta	Placenta
44	chr4:122724000-122740400	Strong transcription	NH-A	brain
45	chr4:122724000-122741800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr4:122724000-122742600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:122724000-122743400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr4:122724200-122729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr4:122724200-122729600	Strong transcription	HSMM	muscle
50	chr4:122724200-122736000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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