Variant report

Variant	rs5749144
Chromosome Location	chr22:31024697-31024698
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005887	0.82[CHB][hapmap]
rs10439913	0.82[AMR][1000 genomes]
rs1076301	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12159167	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13056901	0.82[AMR][1000 genomes]
rs1801198	0.81[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs1971653	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981590	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1981591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072194	0.82[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2078976	0.81[ASN][1000 genomes]
rs2240002	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs2267163	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs2267164	0.82[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2270013	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301956	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3179442	0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs3887855	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4375972	0.83[ASN][1000 genomes]
rs4513384	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820023	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4820891	0.92[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5019308	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749141	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749147	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749149	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753228	0.88[AMR][1000 genomes]
rs5753236	0.87[JPT][hapmap];0.81[AMR][1000 genomes]
rs5753250	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5753252	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753259	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5753265	0.81[ASN][1000 genomes]
rs5994328	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5997704	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs5997711	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997714	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997715	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs713853	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs757027	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8139950	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv966048	chr22:31023818-31024988	Weak transcription Enhancers Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
5	nsv829172	chr22:31024057-31032291	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs5749144	DUSP18	cis	lymphoblastoid	seeQTL
rs5749144	PES1	cis	parietal	SCAN
rs5749144	MORC2	cis	cerebellum	SCAN
rs5749144	TCN2	cis	multi-tissue	Pritchard
rs5749144	LIF	cis	parietal	SCAN
rs5749144	GAL3ST1	cis	cerebellum	SCAN
rs5749144	MTMR3	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31003200-31031200	Weak transcription	Aorta	Aorta
2	chr22:31003800-31030600	Weak transcription	Thymus	Thymus
3	chr22:31006000-31030400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr22:31006000-31030600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:31006000-31030600	Weak transcription	Colonic Mucosa	Colon
6	chr22:31006200-31030600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr22:31006600-31030400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr22:31006800-31030200	Weak transcription	Placenta	Placenta
9	chr22:31007000-31030600	Weak transcription	Fetal Brain Male	brain
10	chr22:31007600-31030200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr22:31008000-31030400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr22:31011600-31026000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:31011800-31030200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr22:31011800-31030600	Weak transcription	Right Ventricle	heart
15	chr22:31012000-31030600	Weak transcription	Brain Angular Gyrus	brain
16	chr22:31013600-31030600	Weak transcription	Pancreas	Pancrea
17	chr22:31013800-31030600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:31014000-31030200	Weak transcription	Brain Substantia Nigra	brain
19	chr22:31014000-31030400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr22:31014000-31030800	Weak transcription	Gastric	stomach
21	chr22:31014000-31030800	Weak transcription	Ovary	ovary
22	chr22:31015800-31030600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr22:31015800-31030600	Weak transcription	Fetal Lung	lung
24	chr22:31017000-31030400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr22:31017000-31030600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr22:31017200-31030600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr22:31019000-31030200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr22:31019200-31030200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr22:31019200-31030200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:31019200-31030600	Weak transcription	Colon Smooth Muscle	Colon
31	chr22:31019200-31030600	Weak transcription	Left Ventricle	heart
32	chr22:31019200-31030800	Weak transcription	Lung	lung
33	chr22:31021600-31026400	Enhancers	Fetal Heart	heart
34	chr22:31022400-31025000	Enhancers	HUVEC	blood vessel
35	chr22:31023000-31030600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr22:31023000-31030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr22:31023000-31030600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr22:31023000-31030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr22:31023200-31024800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr22:31023200-31026000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:31023200-31026000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr22:31023200-31029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr22:31023200-31029600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr22:31023200-31030200	Weak transcription	Fetal Stomach	stomach
45	chr22:31023200-31030400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr22:31023200-31030400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr22:31023200-31030400	Weak transcription	Liver	Liver
48	chr22:31023200-31030600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr22:31023200-31030600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr22:31023200-31030600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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