Variant report

Variant	rs7707965
Chromosome Location	chr5:80119722-80119723
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	chr5:80115178..80117813-chr5:80119510..80121448,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11950254	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11956599	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12515548	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12518711	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12521389	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12521539	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12522132	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12522474	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13154537	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13168327	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13178892	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13179210	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13186354	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1679115	0.86[ASN][1000 genomes]
rs168653	0.84[ASN][1000 genomes]
rs2306371	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs245340	0.80[ASN][1000 genomes]
rs245341	0.81[ASN][1000 genomes]
rs245348	0.84[ASN][1000 genomes]
rs245355	0.85[ASN][1000 genomes]
rs245356	0.85[ASN][1000 genomes]
rs245357	0.85[ASN][1000 genomes]
rs245360	0.85[ASN][1000 genomes]
rs245373	0.82[ASN][1000 genomes]
rs245374	0.84[ASN][1000 genomes]
rs245379	0.82[ASN][1000 genomes]
rs245380	0.80[ASN][1000 genomes]
rs245385	0.84[ASN][1000 genomes]
rs245386	0.82[ASN][1000 genomes]
rs26278	0.86[ASN][1000 genomes]
rs27366	0.83[ASN][1000 genomes]
rs2897298	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32988	0.86[ASN][1000 genomes]
rs32989	0.86[ASN][1000 genomes]
rs32999	0.82[ASN][1000 genomes]
rs34205517	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34274010	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34560430	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34799825	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34816304	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34976588	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35109637	0.86[EUR][1000 genomes]
rs35688814	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35856198	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35967780	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36160284	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3776976	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776977	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776978	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3797898	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs39626	0.87[ASN][1000 genomes]
rs40591	0.83[ASN][1000 genomes]
rs4293894	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58825743	0.80[EUR][1000 genomes]
rs59360125	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59568430	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151888	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151896	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6151904	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151907	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151919	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6151923	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66821541	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6863363	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6874652	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6877065	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72767323	0.86[EUR][1000 genomes]
rs7708096	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7721813	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs888867	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7707965	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
2	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:80091400-80124600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:80091400-80124600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:80091400-80124600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
13	chr5:80091800-80125200	Weak transcription	Osteobl	bone
14	chr5:80093000-80124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:80093800-80123800	Weak transcription	Pancreas	Pancrea
16	chr5:80094800-80124000	Weak transcription	GM12878-XiMat	blood
17	chr5:80097000-80124400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:80097600-80121400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:80097600-80121600	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:80097800-80121600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:80098400-80121600	Weak transcription	Brain Anterior Caudate	brain
22	chr5:80099200-80121400	Weak transcription	Fetal Lung	lung
23	chr5:80103800-80144600	Weak transcription	Gastric	stomach
24	chr5:80107200-80123800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:80109800-80119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:80109800-80121600	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:80110000-80123800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:80110000-80124800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:80110600-80124600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:80110600-80145200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:80110800-80124200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:80110800-80124400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:80110800-80124600	Weak transcription	Placenta	Placenta
34	chr5:80110800-80124800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:80111000-80123600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:80111000-80123600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:80111000-80123800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr5:80111000-80124000	Weak transcription	HepG2	liver
39	chr5:80111400-80124600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr5:80111400-80131800	Weak transcription	Hela-S3	cervix
41	chr5:80111600-80124200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:80112000-80123800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr5:80112200-80124400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:80113200-80123800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr5:80113200-80124000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr5:80113200-80125200	Weak transcription	Fetal Kidney	kidney
47	chr5:80113200-80128200	Weak transcription	HSMM	muscle
48	chr5:80114000-80124600	Weak transcription	Fetal Stomach	stomach
49	chr5:80116800-80121600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr5:80117000-80119800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links