Variant report

Variant	rs5743030
Chromosome Location	chr2:190678545-190678546
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	GATA3	chr2:190678329-190678552	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190666669..190670194-chr2:190675101..190678586,3	MCF-7	breast:
2	chr2:190675814..190678803-chr2:190682468..190684983,2	MCF-7	breast:

Variant related genes	Relation type
PMS1	TF binding region
ENSG00000064933	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1030136	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs12053254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618246	0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs12618262	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs16832155	0.86[EUR][1000 genomes]
rs16832158	0.88[EUR][1000 genomes]
rs2284865	0.88[ASN][1000 genomes]
rs3762543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3791767	0.84[MKK][hapmap];0.86[YRI][hapmap]
rs3791770	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs3791773	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs3828267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4666782	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4666783	0.84[ASW][hapmap];0.86[YRI][hapmap]
rs4667304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4853634	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4920654	0.86[EUR][1000 genomes]
rs4920657	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs4920660	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs4920662	0.86[EUR][1000 genomes]
rs5742933	0.82[YRI][hapmap]
rs5742967	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[ASN][1000 genomes]
rs5742981	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs5743004	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs5743032	0.80[AFR][1000 genomes]
rs5743044	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743100	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[EUR][1000 genomes]
rs5743112	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs5743116	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs5743117	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs5743202	0.91[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs5743208	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6707560	0.86[CHD][hapmap]
rs6736360	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs733318	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs73979023	0.89[EUR][1000 genomes]
rs73979024	0.89[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	nsv3080	chr2:190661654-190706515	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Subcutaneous adipose tissue	22589738	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5743030	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs5743030	ORMDL1	cis	lymphoblastoid	seeQTL
rs5743030	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs5743030	ORMDL1	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649800-190713400	Weak transcription	Gastric	stomach
2	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:190650400-190686800	Weak transcription	Thymus	Thymus
4	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
5	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:190650600-190683200	Weak transcription	Fetal Brain Male	brain
8	chr2:190650600-190688800	Weak transcription	Fetal Heart	heart
9	chr2:190650600-190693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:190650600-190700400	Weak transcription	Hela-S3	cervix
11	chr2:190656800-190685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:190659000-190685000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:190659200-190681200	Weak transcription	Spleen	Spleen
16	chr2:190659800-190686800	Weak transcription	Fetal Stomach	stomach
17	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:190661400-190717800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:190662600-190683000	Weak transcription	Adipose Nuclei	Adipose
20	chr2:190662600-190686800	Weak transcription	Left Ventricle	heart
21	chr2:190662800-190719000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:190663000-190682600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:190663000-190682800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:190663000-190683000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:190663000-190685600	Weak transcription	Brain Anterior Caudate	brain
26	chr2:190663000-190701600	Weak transcription	Psoas Muscle	Psoas
27	chr2:190663000-190712800	Weak transcription	Aorta	Aorta
28	chr2:190663200-190683000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:190663200-190700600	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:190663200-190712400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:190663400-190683400	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:190664600-190680000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:190664600-190683600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:190664800-190686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
36	chr2:190665000-190683000	Weak transcription	HUVEC	blood vessel
37	chr2:190665000-190684400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:190665000-190696600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:190666600-190683600	Strong transcription	HSMM	muscle
40	chr2:190667400-190683200	Weak transcription	NHLF	lung
41	chr2:190667600-190683600	Weak transcription	HMEC	breast
42	chr2:190667800-190686800	Weak transcription	Pancreas	Pancrea
43	chr2:190668400-190684400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:190669400-190683800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:190669400-190686800	Weak transcription	Lung	lung
46	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:190669600-190679400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:190669600-190709600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:190669600-190713200	Weak transcription	Ovary	ovary
50	chr2:190669800-190679800	Weak transcription	Fetal Muscle Trunk	muscle

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