Variant report

Variant	rs1507996
Chromosome Location	chr4:122745729-122745730
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	MXI1	chr4:122743533-122745750	IMR90	lung:	n/a	n/a
2	TAL1	chr4:122743798-122745738	K562	blood:	n/a	n/a
3	POLR2A	chr4:122743956-122745788	PFSK-1	brain:	n/a	n/a
4	NRF1	chr4:122744434-122745789	SK-N-SH	brain:	n/a	chr4:122745218-122745229 chr4:122745220-122745229
5	POLR2A	chr4:122744684-122745753	U87	brain:	n/a	n/a
6	POLR2A	chr4:122743909-122745757	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr4:122743601-122745767	GM12891	blood:	n/a	n/a
8	ARID3A	chr4:122745073-122745747	K562	blood:	n/a	n/a
9	POLR2A	chr4:122744056-122745753	U87	brain:	n/a	n/a
10	E2F4	chr4:122743998-122746113	MCF10A-Er-Src	breast:	n/a	chr4:122744271-122744278 chr4:122744970-122744977 chr4:122745112-122745121 chr4:122745110-122745119 chr4:122745219-122745228 chr4:122745205-122745217
11	POLR2A	chr4:122745710-122745781	GM12878	blood:	n/a	n/a
12	MXI1	chr4:122743372-122745865	SK-N-SH	brain:	n/a	n/a
13	RFX5	chr4:122744719-122745817	SK-N-SH	brain:	n/a	n/a
14	ESRRA	chr4:122744696-122745966	GM12878	blood:	n/a	n/a
15	MXI1	chr4:122744874-122745740	K562	blood:	n/a	n/a
16	IRF1	chr4:122744851-122745807	K562	blood:	n/a	chr4:122745172-122745186 chr4:122745227-122745241

No.	Distal block	Cell Line	Cell type
1	chr4:122745296..122747989-chr4:122762768..122765096,2	K562	blood:
2	chr4:122745115..122747989-chr4:122763596..122768679,4	K562	blood:
3	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
4	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:

Variant related genes	Relation type
CCNA2	TF binding region
ENSG00000123737	Chromatin interaction
ENSG00000138686	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12650359	0.94[ASN][1000 genomes]
rs6813653	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824258	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1507996	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122743400-122745800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr4:122743600-122745800	Active TSS	Fetal Intestine Large	intestine
3	chr4:122743600-122745800	Active TSS	NHDF-Ad	bronchial
4	chr4:122743800-122745800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:122743800-122745800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:122743800-122745800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:122743800-122745800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:122743800-122745800	Active TSS	GM12878-XiMat	blood
9	chr4:122744000-122745800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr4:122744000-122745800	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr4:122744000-122745800	Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr4:122744000-122745800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr4:122744000-122745800	Active TSS	A549	lung
14	chr4:122744200-122746200	Active TSS	K562	blood
15	chr4:122744400-122745800	Active TSS	Brain Angular Gyrus	brain
16	chr4:122744400-122745800	Active TSS	Placenta Amnion	Placenta Amnion
17	chr4:122744400-122746000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:122744600-122745800	Active TSS	Primary monocytes fromperipheralblood	blood
19	chr4:122744600-122745800	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr4:122744600-122745800	Active TSS	Brain Cingulate Gyrus	brain
21	chr4:122744600-122745800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:122744600-122745800	Active TSS	Brain Substantia Nigra	brain
23	chr4:122744600-122745800	Active TSS	Fetal Lung	lung
24	chr4:122744600-122745800	Active TSS	Fetal Stomach	stomach
25	chr4:122744600-122745800	Active TSS	HMEC	breast
26	chr4:122744600-122746400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr4:122744800-122745800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:122744800-122745800	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr4:122744800-122745800	Active TSS	Primary hematopoietic stem cells	blood
30	chr4:122744800-122745800	Active TSS	Brain Anterior Caudate	brain
31	chr4:122744800-122745800	Active TSS	Brain Germinal Matrix	brain
32	chr4:122744800-122745800	Active TSS	Brain Hippocampus Middle	brain
33	chr4:122744800-122745800	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr4:122744800-122745800	Active TSS	Fetal Muscle Leg	muscle
35	chr4:122745000-122745800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:122745000-122745800	Active TSS	Fetal Brain Female	brain
37	chr4:122745000-122745800	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr4:122745000-122745800	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr4:122745000-122745800	Active TSS	Stomach Smooth Muscle	stomach
40	chr4:122745000-122745800	Active TSS	HepG2	liver
41	chr4:122745200-122745800	Active TSS	Fetal Brain Male	brain
42	chr4:122745400-122745800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr4:122745400-122745800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr4:122745400-122745800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:122745400-122745800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr4:122745400-122745800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr4:122745400-122745800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr4:122745400-122745800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr4:122745400-122745800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:122745400-122745800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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