Variant report

Variant	rs3737522
Chromosome Location	chr1:159021445-159021446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:159021267..159022786-chr1:159028337..159030656,2	K562	blood:

Variant related genes	Relation type
ENSG00000265589	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1057027	0.82[CHD][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs1057028	0.82[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs1101998	0.85[GIH][hapmap]
rs11265134	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12094741	0.88[GIH][hapmap]
rs12098223	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124059	0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1616024	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1633256	0.82[CHD][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1633266	0.80[CEU][hapmap];0.90[EUR][1000 genomes]
rs1633267	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16841642	0.90[CHD][hapmap]
rs1772407	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1772408	0.86[GIH][hapmap]
rs1772414	0.93[CHD][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1772415	0.90[CHD][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs1935067	0.90[CHD][hapmap]
rs2236584	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298803	0.87[CHD][hapmap]
rs2518555	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518562	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2570916	0.86[GIH][hapmap]
rs2793844	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793845	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2852695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754460	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768514	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768519	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768523	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74122214	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74122232	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7532207	1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs855865	0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs856054	0.82[CEU][hapmap]
rs856055	0.94[GIH][hapmap];0.81[TSI][hapmap]
rs861318	0.91[GIH][hapmap];0.81[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3737522	IFI16	cis	parietal	SCAN
rs3737522	OR10R2	cis	parietal	SCAN
rs3737522	TMEM79	cis	parietal	SCAN
rs3737522	AIM2	cis	lymphoblastoid	seeQTL
rs3737522	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs3737522	IFI16	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
3	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
5	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:158998400-159024000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
10	chr1:158999000-159022800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:158999200-159023800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:159000000-159026200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:159000400-159024200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:159000600-159023800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:159001000-159027400	Weak transcription	Right Ventricle	heart
16	chr1:159001400-159024200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:159001400-159036200	Weak transcription	Small Intestine	intestine
18	chr1:159001600-159028400	Strong transcription	Fetal Thymus	thymus
19	chr1:159003000-159022000	Weak transcription	Fetal Brain Male	brain
20	chr1:159004600-159022800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:159005400-159023200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:159005600-159027200	Weak transcription	Brain Angular Gyrus	brain
23	chr1:159006800-159024200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:159007200-159026800	Weak transcription	Pancreas	Pancrea
25	chr1:159009000-159023000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:159009000-159026400	Strong transcription	Dnd41	blood
27	chr1:159009200-159030400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:159010600-159023800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:159010600-159026400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:159011400-159022800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:159011400-159023800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:159011400-159024000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:159011600-159023800	Strong transcription	Osteobl	bone
34	chr1:159013000-159025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:159015200-159023800	Strong transcription	HSMM	muscle
36	chr1:159016400-159024800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:159016600-159023400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:159016600-159023800	Weak transcription	Stomach Mucosa	stomach
39	chr1:159016800-159023600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:159017000-159023000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:159017000-159025600	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:159017000-159026800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:159017600-159023200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:159017800-159023800	Strong transcription	HMEC	breast
45	chr1:159018000-159024400	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:159018000-159026000	Strong transcription	Hela-S3	cervix
47	chr1:159018200-159024000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr1:159018200-159026200	Strong transcription	Ovary	ovary
49	chr1:159019200-159024000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:159019400-159022800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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