Variant report

Variant	rs13418158
Chromosome Location	chr2:190640434-190640435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:190640337-190640514	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190639387..190641979-chr2:190643481..190646316,2	K562	blood:
2	chr2:190639477..190641367-chr2:190643907..190646225,2	MCF-7	breast:
3	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
4	chr2:190634458..190636965-chr2:190638954..190642659,3	MCF-7	breast:
5	chr2:190640380..190645016-chr2:190647065..190650284,8	MCF-7	breast:
6	chr2:190639322..190641335-chr2:190649271..190651460,2	K562	blood:

No data

Variant related genes	Relation type
ORMDL1	TF binding region
ENSG00000128699	Chromatin interaction
ENSG00000064933	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10176506	1.00[AMR][1000 genomes]
rs10197551	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197577	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10497706	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13390239	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13400261	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404356	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411095	0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416709	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418043	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418434	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13429804	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831975	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2118453	0.89[AFR][1000 genomes]
rs5742923	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742932	1.00[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742935	1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742979	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743009	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs5743026	0.84[AFR][1000 genomes]
rs5743042	0.84[AFR][1000 genomes]
rs5743064	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs5743075	0.83[YRI][hapmap]
rs5743176	0.84[YRI][hapmap]
rs57785091	0.89[AFR][1000 genomes]
rs6711817	0.89[AFR][1000 genomes]
rs6746951	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760126	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048418	0.89[AFR][1000 genomes]
rs73048420	0.89[AFR][1000 genomes]
rs73048432	0.89[AFR][1000 genomes]
rs73048437	0.89[AFR][1000 genomes]
rs73048445	0.92[AFR][1000 genomes]
rs73049960	0.88[AFR][1000 genomes]
rs73050376	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7560735	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7577159	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs7583918	1.00[AMR][1000 genomes]
rs7600993	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13418158	PMS1	cis	multi-tissue	Pritchard
rs13418158	PMS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190627800-190642800	Weak transcription	Spleen	Spleen
2	chr2:190627800-190648200	Weak transcription	Gastric	stomach
3	chr2:190628200-190642800	Weak transcription	Lung	lung
4	chr2:190628200-190643200	Weak transcription	Esophagus	oesophagus
5	chr2:190628200-190645600	Weak transcription	Pancreas	Pancrea
6	chr2:190628200-190648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:190628200-190648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:190628200-190648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:190628400-190642800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:190628400-190648000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:190628600-190642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:190628600-190642800	Weak transcription	Fetal Intestine Small	intestine
13	chr2:190628600-190642800	Weak transcription	Thymus	Thymus
14	chr2:190628600-190647000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:190628600-190647200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:190628600-190647200	Weak transcription	Stomach Mucosa	stomach
17	chr2:190628600-190648400	Weak transcription	Small Intestine	intestine
18	chr2:190628800-190642800	Weak transcription	Fetal Stomach	stomach
19	chr2:190629000-190644200	Weak transcription	Fetal Brain Male	brain
20	chr2:190629000-190647200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:190629800-190647000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:190630000-190646600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:190630800-190647000	Strong transcription	HSMM	muscle
24	chr2:190631000-190646200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:190631200-190645400	Strong transcription	Liver	Liver
26	chr2:190631200-190646200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:190631200-190647200	Strong transcription	Fetal Thymus	thymus
28	chr2:190631400-190642200	Strong transcription	NHDF-Ad	bronchial
29	chr2:190631400-190644000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:190631400-190646000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:190631400-190646000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:190631400-190646800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:190631600-190645000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:190631600-190645600	Strong transcription	Primary B cells from cord blood	blood
35	chr2:190631600-190646200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:190631600-190647000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:190632000-190646600	Strong transcription	Placenta	Placenta
38	chr2:190632800-190642600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:190632800-190647200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:190633000-190645200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:190633200-190646200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:190633200-190646800	Strong transcription	HMEC	breast
43	chr2:190633600-190642800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:190633600-190646600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:190634000-190646400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:190634000-190647000	Strong transcription	Osteobl	bone
47	chr2:190634200-190641800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:190634200-190644800	Strong transcription	Fetal Intestine Large	intestine
49	chr2:190634200-190647400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:190634400-190644200	Strong transcription	Dnd41	blood

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