Variant report

Variant	rs7600993
Chromosome Location	chr2:190687929-190687930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10197551	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10197577	1.00[ASW][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10209952	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10210548	1.00[AMR][1000 genomes]
rs10497706	1.00[YRI][hapmap]
rs13408971	1.00[AMR][1000 genomes]
rs13411095	0.95[YRI][hapmap]
rs13416709	0.95[YRI][hapmap]
rs13418043	0.95[YRI][hapmap]
rs13418158	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs13418171	1.00[AMR][1000 genomes]
rs13429804	1.00[YRI][hapmap]
rs13432549	1.00[AMR][1000 genomes]
rs16831975	1.00[YRI][hapmap]
rs28367047	1.00[AMR][1000 genomes]
rs5742923	1.00[ASW][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs5742932	0.80[LWK][hapmap];0.90[YRI][hapmap]
rs5742935	0.80[LWK][hapmap];0.90[YRI][hapmap]
rs5742944	0.80[AFR][1000 genomes]
rs5742979	0.90[YRI][hapmap]
rs5743009	0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743018	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743026	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743042	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743064	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743071	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743075	0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5743176	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs5743195	1.00[AMR][1000 genomes]
rs6746951	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6760126	0.90[YRI][hapmap]
rs7355626	1.00[AMR][1000 genomes]
rs7577159	0.90[YRI][hapmap]
rs9630990	1.00[AMR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7600993	PMS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 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	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
4	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:190650600-190688800	Weak transcription	Fetal Heart	heart
7	chr2:190650600-190693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:190650600-190700400	Weak transcription	Hela-S3	cervix
9	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:190661400-190717800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:190662800-190719000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:190663000-190701600	Weak transcription	Psoas Muscle	Psoas
15	chr2:190663000-190712800	Weak transcription	Aorta	Aorta
16	chr2:190663200-190700600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:190663200-190712400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
19	chr2:190665000-190696600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:190669600-190709600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:190669600-190713200	Weak transcription	Ovary	ovary
23	chr2:190669800-190709000	Weak transcription	Placenta	Placenta
24	chr2:190670800-190712800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:190671000-190719600	Weak transcription	NH-A	brain
26	chr2:190675400-190690200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:190675400-190693800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:190676200-190712400	Weak transcription	K562	blood
29	chr2:190676400-190690400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:190677000-190709400	Weak transcription	Fetal Intestine Small	intestine
31	chr2:190677400-190689800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:190681000-190743000	Weak transcription	Brain Germinal Matrix	brain
33	chr2:190682400-190690600	Weak transcription	Brain Substantia Nigra	brain
34	chr2:190683800-190709800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:190684000-190690400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:190684000-190690400	Weak transcription	NHEK	skin
37	chr2:190684000-190692200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:190684000-190693600	Weak transcription	NHLF	lung
39	chr2:190684000-190693800	Weak transcription	Fetal Kidney	kidney
40	chr2:190684000-190700400	Weak transcription	A549	lung
41	chr2:190684000-190712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:190684000-190712800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:190684000-190743600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:190684200-190690400	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:190684200-190693000	Weak transcription	HSMM	muscle
46	chr2:190684400-190698800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:190684400-190700600	Weak transcription	Fetal Brain Male	brain
48	chr2:190684600-190690600	Weak transcription	HUVEC	blood vessel
49	chr2:190684600-190709800	Weak transcription	HMEC	breast
50	chr2:190684600-190712600	Weak transcription	Primary hematopoietic stem cells	blood

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