Variant report

Variant	rs6746951
Chromosome Location	chr2:190644513-190644514
allele	A/C
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	chr2:190643853-190644766	GM12878	blood:	n/a	n/a
2	NFYB	chr2:190644375-190644527	Hela-S3	cervix:	n/a	n/a

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	chr2:190637903..190640151-chr2:190642626..190644540,2	MCF-7	breast:
4	chr2:190640380..190645016-chr2:190647065..190650284,8	MCF-7	breast:

Variant related genes	Relation type
PMS1	TF binding region
ENSG00000231145	TF binding region
ENSG00000128699	Chromatin interaction
ENSG00000064933	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10176506	1.00[AMR][1000 genomes]
rs10197551	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10197577	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10497706	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13390239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13400261	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13404356	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13411095	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416709	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418043	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418158	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13418434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13429804	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16831975	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2118453	0.88[AFR][1000 genomes]
rs5742923	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742932	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742935	0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742979	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743009	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs5743026	0.83[AFR][1000 genomes]
rs5743042	0.83[AFR][1000 genomes]
rs5743064	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs5743176	0.83[YRI][hapmap]
rs57785091	0.88[AFR][1000 genomes]
rs6711817	0.88[AFR][1000 genomes]
rs6760126	0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048418	0.88[AFR][1000 genomes]
rs73048420	0.88[AFR][1000 genomes]
rs73048432	0.88[AFR][1000 genomes]
rs73048437	0.88[AFR][1000 genomes]
rs73048445	0.91[AFR][1000 genomes]
rs73049960	0.87[AFR][1000 genomes]
rs73050376	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7560735	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7577159	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs7583918	1.00[AMR][1000 genomes]
rs7600993	1.00[YRI][hapmap];0.80[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6746951	PMS1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190627800-190648200	Weak transcription	Gastric	stomach
2	chr2:190628200-190645600	Weak transcription	Pancreas	Pancrea
3	chr2:190628200-190648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:190628200-190648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:190628200-190648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:190628400-190648000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:190628600-190647000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:190628600-190647200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:190628600-190647200	Weak transcription	Stomach Mucosa	stomach
10	chr2:190628600-190648400	Weak transcription	Small Intestine	intestine
11	chr2:190629000-190647200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:190629800-190647000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:190630000-190646600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:190630800-190647000	Strong transcription	HSMM	muscle
15	chr2:190631000-190646200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:190631200-190645400	Strong transcription	Liver	Liver
17	chr2:190631200-190646200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:190631200-190647200	Strong transcription	Fetal Thymus	thymus
19	chr2:190631400-190646000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:190631400-190646000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:190631400-190646800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:190631600-190645000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:190631600-190645600	Strong transcription	Primary B cells from cord blood	blood
24	chr2:190631600-190646200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:190631600-190647000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:190632000-190646600	Strong transcription	Placenta	Placenta
27	chr2:190632800-190647200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr2:190633000-190645200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:190633200-190646200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:190633200-190646800	Strong transcription	HMEC	breast
31	chr2:190633600-190646600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:190634000-190646400	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr2:190634000-190647000	Strong transcription	Osteobl	bone
34	chr2:190634200-190644800	Strong transcription	Fetal Intestine Large	intestine
35	chr2:190634200-190647400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr2:190634600-190644800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr2:190634600-190645000	Strong transcription	Primary T cells from cord blood	blood
38	chr2:190634600-190645800	Strong transcription	Adipose Nuclei	Adipose
39	chr2:190634600-190646200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr2:190634600-190646400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:190634600-190646600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr2:190634600-190647000	Strong transcription	NH-A	brain
43	chr2:190634600-190647200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:190634600-190647200	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:190634600-190647200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:190634800-190645200	Strong transcription	HUVEC	blood vessel
47	chr2:190635000-190647000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:190635000-190647200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:190635200-190645200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:190635200-190645800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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