Variant report

Variant	rs2292984
Chromosome Location	chr4:57190115-57190116
allele	C/T
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	EGR1	chr4:57190082-57190388	K562	blood:	n/a	chr4:57190094-57190107 chr4:57190258-57190268

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57188347..57191240-chr4:57253035..57255608,2	K562	blood:

Variant related genes	Relation type
MRPL22P1	TF binding region
ENSG00000269921	Chromatin interaction
ENSG00000157426	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1401908	1.00[JPT][hapmap]
rs17086746	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17086755	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17086769	0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs17086776	0.92[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17086786	0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs17086844	0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs17086879	1.00[EUR][1000 genomes]
rs17086893	1.00[EUR][1000 genomes]
rs17086906	1.00[EUR][1000 genomes]
rs17086908	1.00[EUR][1000 genomes]
rs17086924	1.00[EUR][1000 genomes]
rs28649329	1.00[EUR][1000 genomes]
rs34228795	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34543011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3796543	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074775	0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs41476944	0.92[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs57439970	1.00[EUR][1000 genomes]
rs58337902	1.00[EUR][1000 genomes]
rs59161426	0.86[ASN][1000 genomes]
rs61580407	1.00[EUR][1000 genomes]
rs61732641	1.00[EUR][1000 genomes]
rs73155895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73155901	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157733	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157739	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157754	1.00[EUR][1000 genomes]
rs73157769	1.00[EUR][1000 genomes]
rs73157772	1.00[EUR][1000 genomes]
rs73157774	1.00[EUR][1000 genomes]
rs73157784	1.00[EUR][1000 genomes]
rs73159954	0.93[ASN][1000 genomes]
rs73159959	0.97[ASN][1000 genomes]
rs73159992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73162272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73167378	1.00[EUR][1000 genomes]
rs73167396	1.00[EUR][1000 genomes]
rs7437329	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2292984	ARL9	cis	multi-tissue	Pritchard
rs2292984	ARL9	cis	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
3	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
6	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
7	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:57178000-57190400	Weak transcription	Brain Angular Gyrus	brain
10	chr4:57178200-57190200	Weak transcription	Brain Substantia Nigra	brain
11	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:57178600-57190200	Weak transcription	Fetal Brain Male	brain
13	chr4:57180800-57191800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:57180800-57197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:57181200-57196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:57181400-57203800	Weak transcription	HSMMtube	muscle
17	chr4:57181800-57191200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:57181800-57196200	Strong transcription	Fetal Intestine Large	intestine
19	chr4:57182800-57196800	Weak transcription	Ovary	ovary
20	chr4:57183000-57190200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:57183000-57193800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:57183200-57194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:57186600-57190400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr4:57187200-57202600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:57187600-57191400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:57187800-57192400	Weak transcription	HUVEC	blood vessel
28	chr4:57188400-57190800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr4:57188400-57203600	Weak transcription	Fetal Lung	lung
30	chr4:57188600-57192800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:57188600-57197800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:57189000-57195800	Strong transcription	Brain Germinal Matrix	brain
33	chr4:57189200-57190600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:57189200-57190800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:57189200-57190800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:57189200-57191800	Strong transcription	Fetal Brain Female	brain
37	chr4:57189400-57190400	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr4:57189400-57190400	Genic enhancers	Fetal Stomach	stomach
39	chr4:57189400-57192000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:57189400-57195800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr4:57189600-57190200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:57189600-57190800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:57189600-57190800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:57189600-57191000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:57189600-57191000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:57189600-57192800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:57189600-57194000	Weak transcription	Placenta	Placenta
48	chr4:57189800-57190400	Enhancers	Brain Anterior Caudate	brain
49	chr4:57189800-57190600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:57189800-57190800	Strong transcription	H1 Cell Line	embryonic stem cell

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