Variant report

Variant	rs5749199
Chromosome Location	chr22:31325742-31325743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31323613..31326465-chr22:31353676..31355582,2	K562	blood:
2	chr22:31324433..31326131-chr22:31327811..31329834,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133422	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10854601	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11089484	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12167144	0.85[AMR][1000 genomes]
rs12168307	0.83[AMR][1000 genomes]
rs1807686	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2016654	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2019182	0.80[EUR][1000 genomes]
rs2072132	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2074578	0.80[AFR][1000 genomes]
rs2079221	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240175	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240177	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240179	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240180	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240183	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3747151	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3788426	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804084	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3804085	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3948685	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4820916	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4820923	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4820925	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4820926	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5749185	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5749189	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5749192	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5749201	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5753378	0.80[AMR][1000 genomes]
rs5753379	0.80[AMR][1000 genomes]
rs5753383	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753386	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753388	0.81[AFR][1000 genomes]
rs5753389	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753394	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753396	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5753398	0.80[AFR][1000 genomes]
rs5753407	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753408	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753410	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5997807	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997830	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997838	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6518726	0.82[EUR][1000 genomes]
rs722683	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs722684	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7284767	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7289831	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7290078	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7291199	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7291361	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs737924	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737926	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737927	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs739896	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8004	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8135974	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9609183	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9609185	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9609188	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9609193	0.81[EUR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5749199	MORC2-AS1	cis	Nerve Tibial	GTEx
rs5749199	MORC2-AS1	cis	Thyroid	GTEx
rs5749199	TUG1	Cis_1M	lymphoblastoid	RTeQTL
rs5749199	MORC2-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31317600-31364000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:31318400-31342200	Weak transcription	Right Atrium	heart
3	chr22:31318600-31328000	Weak transcription	Fetal Heart	heart
4	chr22:31318600-31329000	Weak transcription	Stomach Mucosa	stomach
5	chr22:31319000-31333200	Strong transcription	Primary T cells from cord blood	blood
6	chr22:31319000-31343600	Strong transcription	Fetal Stomach	stomach
7	chr22:31319200-31338600	Strong transcription	Thymus	Thymus
8	chr22:31319200-31344000	Strong transcription	Fetal Intestine Small	intestine
9	chr22:31319200-31345200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr22:31319200-31347400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr22:31319200-31350800	Strong transcription	Brain Germinal Matrix	brain
12	chr22:31319200-31351800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr22:31319400-31327600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr22:31319400-31336400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:31319400-31337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr22:31319400-31342200	Strong transcription	Fetal Muscle Leg	muscle
17	chr22:31319600-31326000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr22:31319600-31327000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr22:31319600-31342000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr22:31319600-31342200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr22:31319600-31343200	Strong transcription	Placenta	Placenta
22	chr22:31319600-31345200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr22:31319800-31342200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:31319800-31343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:31319800-31343200	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr22:31319800-31353200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr22:31319800-31355800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr22:31320000-31342000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr22:31320000-31342200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr22:31320000-31342400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr22:31320000-31344000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:31320000-31354600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr22:31320000-31355600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr22:31320200-31336400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr22:31320200-31336800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr22:31320200-31340200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr22:31320200-31342200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr22:31320200-31343000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr22:31320200-31353400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr22:31320200-31354800	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr22:31320200-31355600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr22:31320200-31355800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr22:31320400-31336800	Strong transcription	Lung	lung
44	chr22:31320400-31340600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr22:31320400-31342400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr22:31320400-31345200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr22:31320600-31325800	Strong transcription	Adipose Nuclei	Adipose
48	chr22:31320600-31336600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr22:31320600-31336800	Strong transcription	Spleen	Spleen
50	chr22:31320600-31343600	Strong transcription	Duodenum Mucosa	Duodenum

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