Variant report

Variant	rs56137655
Chromosome Location	chr2:190540570-190540571
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	POLR2A	chr2:190540500-190540617	HepG2	liver:	n/a	n/a
2	USF1	chr2:190540542-190540731	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:190540172-190540616	HepG2	liver:	n/a	n/a
4	WRNIP1	chr2:190540525-190540590	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190538834..190541562-chr2:190626367..190628350,2	MCF-7	breast:

Variant related genes	Relation type
ANKAR	TF binding region
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16831821	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831873	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831944	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831972	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17271246	0.86[EUR][1000 genomes]
rs2164830	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2278591	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289405	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56324258	0.85[EUR][1000 genomes]
rs5742926	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs5742985	0.87[EUR][1000 genomes]
rs5743047	0.85[EUR][1000 genomes]
rs5743077	0.81[EUR][1000 genomes]
rs62183651	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183652	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183653	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62183656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183657	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62183658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62183659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62184265	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62184267	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62184268	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62185869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62185872	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62185874	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62185897	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6726636	0.83[EUR][1000 genomes]
rs72920421	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56137655	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs56137655	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs56137655	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs56137655	ORMDL1	cis	Muscle Skeletal	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:190530000-190542800	Strong transcription	Dnd41	blood
3	chr2:190534000-190550200	Weak transcription	K562	blood
4	chr2:190539200-190540600	Active TSS	Hela-S3	cervix
5	chr2:190539400-190540600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr2:190539600-190540600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:190539600-190543400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:190539800-190540600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:190539800-190550200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:190539800-190550200	Weak transcription	Esophagus	oesophagus
11	chr2:190539800-190550200	Weak transcription	Small Intestine	intestine
12	chr2:190540000-190540600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:190540000-190540600	Active TSS	Primary T cells from cord blood	blood
14	chr2:190540000-190540600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:190540000-190540600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:190540000-190540600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:190540000-190540600	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr2:190540000-190540600	Enhancers	Fetal Heart	heart
19	chr2:190540000-190540600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr2:190540000-190540800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:190540000-190540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:190540000-190540800	Enhancers	Lung	lung
23	chr2:190540000-190540800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:190540000-190542400	Weak transcription	Brain Germinal Matrix	brain
25	chr2:190540000-190542600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:190540000-190546000	Weak transcription	Gastric	stomach
27	chr2:190540000-190546000	Weak transcription	Left Ventricle	heart
28	chr2:190540000-190546000	Weak transcription	Ovary	ovary
29	chr2:190540000-190550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:190540000-190550200	Weak transcription	Fetal Thymus	thymus
31	chr2:190540000-190550400	Weak transcription	Fetal Kidney	kidney
32	chr2:190540000-190563400	Weak transcription	Aorta	Aorta
33	chr2:190540200-190540600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr2:190540200-190540600	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:190540200-190540600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr2:190540200-190540600	Enhancers	Brain Anterior Caudate	brain
37	chr2:190540200-190540600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr2:190540200-190540600	Enhancers	Fetal Lung	lung
39	chr2:190540200-190540600	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr2:190540200-190540800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr2:190540200-190540800	Enhancers	Primary B cells from peripheral blood	blood
42	chr2:190540200-190540800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr2:190540200-190540800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr2:190540200-190540800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr2:190540200-190540800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:190540200-190540800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:190540200-190540800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr2:190540200-190540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:190540200-190540800	Enhancers	Liver	Liver
50	chr2:190540200-190540800	Enhancers	Duodenum Smooth Muscle	Duodenum

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