Variant report

Variant	rs2941522
Chromosome Location	chr17:37910368-37910369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:47)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:47 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37892523..37898235-chr17:37904182..37913977,22	MCF-7	breast:
2	chr17:37909990..37912890-chr17:37955777..37957738,2	MCF-7	breast:
3	chr17:37897334..37903790-chr17:37903988..37910787,11	K562	blood:
4	chr17:37771753..37773281-chr17:37910069..37912599,2	K562	blood:
5	chr17:37823262..37824838-chr17:37908595..37910545,2	K562	blood:
6	chr17:37683291..37684206-chr17:37910150..37911036,3	K562	blood:
7	chr17:37772682..37776519-chr17:37907348..37911982,7	MCF-7	breast:
8	chr17:37891847..37892835-chr17:37910131..37910631,2	MCF-7	breast:
9	chr17:37885072..37889612-chr17:37908286..37912584,6	MCF-7	breast:
10	chr17:37907935..37911541-chr17:37914774..37918367,3	K562	blood:
11	chr17:37909095..37912398-chr17:37915882..37918594,4	MCF-7	breast:
12	chr17:37875233..37878023-chr17:37910337..37912992,2	MCF-7	breast:
13	chr17:37885422..37887892-chr17:37909148..37911946,2	MCF-7	breast:
14	chr17:37808864..37809478-chr17:37910143..37911035,2	K562	blood:
15	chr17:37905061..37908397-chr17:37908549..37911938,4	MCF-7	breast:
16	chr17:37909648..37912266-chr17:38136324..38138333,2	K562	blood:
17	chr17:37761755..37764258-chr17:37910151..37911878,2	K562	blood:
18	chr17:37777961..37778768-chr17:37910171..37911038,7	MCF-7	breast:
19	chr17:37908803..37910895-chr17:38473942..38476553,2	MCF-7	breast:
20	chr17:37908772..37911030-chr17:38098767..38100390,2	K562	blood:
21	chr17:37795949..37798919-chr17:37909347..37911771,2	K562	blood:
22	chr17:37854770..37856284-chr17:37908500..37910494,2	MCF-7	breast:
23	chr17:37909648..37914905-chr17:37919305..37927863,11	MCF-7	breast:
24	chr17:37774213..37778029-chr17:37909285..37912435,4	K562	blood:
25	chr17:37886303..37886819-chr17:37910361..37910999,2	HCT-116	colon:
26	chr17:37777770..37778817-chr17:37910195..37911123,12	MCF-7	breast:
27	chr17:37908791..37912830-chr17:37925750..37930091,5	K562	blood:
28	chr17:37790354..37790890-chr17:37910125..37910633,2	K562	blood:
29	chr17:37810058..37810709-chr17:37910120..37910665,2	K562	blood:
30	chr17:37789315..37792571-chr17:37910228..37913282,4	K562	blood:
31	chr17:37777309..37780105-chr17:37909118..37911531,3	MCF-7	breast:
32	chr17:37616757..37620297-chr17:37908971..37911945,3	K562	blood:
33	chr17:37839354..37839977-chr17:37910043..37910634,2	MCF-7	breast:
34	chr17:37909023..37911172-chr17:38018730..38020894,2	K562	blood:
35	chr17:37895465..37903504-chr17:37904751..37910787,10	K562	blood:
36	chr17:37673655..37675893-chr17:37909404..37912318,2	K562	blood:
37	chr17:37892158..37901988-chr17:37904094..37913282,26	MCF-7	breast:
38	chr17:37803422..37805216-chr17:37908761..37911561,2	K562	blood:
39	chr17:37823299..37826049-chr17:37908764..37910653,3	K562	blood:
40	chr17:37777123..37780362-chr17:37909816..37911514,36	K562	blood:
41	chr17:37886257..37887318-chr17:37910001..37911188,5	MCF-7	breast:
42	chr17:37828636..37830492-chr17:37908075..37910484,2	K562	blood:
43	chr17:37775146..37779845-chr17:37909073..37911911,5	K562	blood:
44	chr17:37790735..37794088-chr17:37909085..37913282,4	K562	blood:
45	chr17:37886436..37886983-chr17:37910213..37911121,2	K562	blood:
46	chr17:37909376..37912567-chr17:37922952..37926689,4	MCF-7	breast:
47	chr17:37909855..37912536-chr17:38125394..38127110,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000131748	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000141744	Chromatin interaction
ENSG00000214546	Chromatin interaction
ENSG00000167258	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000264198	Chromatin interaction
ENSG00000171532	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000161405	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10445308	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658993	0.96[ASN][1000 genomes]
rs12942330	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12944882	0.86[EUR][1000 genomes]
rs12946510	0.99[ASN][1000 genomes]
rs2313430	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952140	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2952144	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816470	0.86[EUR][1000 genomes]
rs4795395	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs907091	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907092	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303277	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9747973	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9909593	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9916765	0.83[AMR][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	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv908219	chr17:37880265-37917633	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv3360194	chr17:37909251-37911799	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2941522	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2941522	IKZF3	cis	multi-tissue	Pritchard
rs2941522	GSDMB	cis	Whole Blood	GTEx
rs2941522	PGAP3	cis	Heart Left Ventricle	GTEx
rs2941522	ORMDL3	cis	multi-tissue	Pritchard
rs2941522	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37908800-37910400	Weak transcription	Fetal Kidney	kidney
2	chr17:37908800-37910800	Weak transcription	Fetal Lung	lung
3	chr17:37909200-37912000	Flanking Active TSS	Dnd41	blood
4	chr17:37909400-37910400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr17:37909400-37910400	Enhancers	Fetal Heart	heart
6	chr17:37909400-37910400	Flanking Active TSS	Pancreas	Pancrea
7	chr17:37909400-37912600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:37909600-37910400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr17:37909600-37910400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr17:37909600-37910600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr17:37909600-37910600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr17:37909600-37911400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr17:37909600-37911800	Active TSS	Rectal Smooth Muscle	rectum
14	chr17:37909800-37910400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr17:37909800-37910400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:37909800-37910400	Flanking Active TSS	Colonic Mucosa	Colon
17	chr17:37909800-37910600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:37909800-37910600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:37909800-37910600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:37909800-37910600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:37909800-37910600	Flanking Active TSS	Right Ventricle	heart
22	chr17:37909800-37910600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr17:37909800-37910800	Active TSS	NHEK	skin
24	chr17:37909800-37911000	Active TSS	Primary T cells from cord blood	blood
25	chr17:37909800-37911200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:37909800-37911200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr17:37909800-37911200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr17:37909800-37911200	Active TSS	Brain Angular Gyrus	brain
29	chr17:37909800-37911200	Active TSS	Thymus	Thymus
30	chr17:37909800-37911200	Active TSS	GM12878-XiMat	blood
31	chr17:37909800-37911400	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr17:37909800-37911400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:37909800-37911400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr17:37909800-37911400	Active TSS	Brain Cingulate Gyrus	brain
35	chr17:37909800-37911400	Active TSS	Left Ventricle	heart
36	chr17:37909800-37911400	Active TSS	Psoas Muscle	Psoas
37	chr17:37909800-37911400	Active TSS	HSMM	muscle
38	chr17:37909800-37911400	Flanking Active TSS	NH-A	brain
39	chr17:37909800-37911400	Active TSS	Osteobl	bone
40	chr17:37909800-37911600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr17:37909800-37911600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr17:37909800-37911600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:37909800-37911800	Active TSS	Brain Anterior Caudate	brain
44	chr17:37909800-37912200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:37910000-37910400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:37910000-37910400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr17:37910000-37910400	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr17:37910000-37910400	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr17:37910000-37910400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:37910000-37910400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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