Variant report

Variant	rs2972361
Chromosome Location	chr5:68560582-68560583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10063757	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10940209	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940210	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10940212	0.82[ASN][1000 genomes]
rs10940216	0.82[ASN][1000 genomes]
rs11744596	0.81[ASN][1000 genomes]
rs11748974	0.89[ASN][1000 genomes]
rs12659146	0.81[ASN][1000 genomes]
rs13175606	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs151589	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs163444	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164709	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs164715	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164789	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1650779	0.87[ASN][1000 genomes]
rs171212	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184747	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976103	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2002825	0.81[ASN][1000 genomes]
rs2130757	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171148	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242350	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2242351	0.81[ASN][1000 genomes]
rs2291519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291520	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450230	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450246	0.85[ASN][1000 genomes]
rs2637128	0.80[ASN][1000 genomes]
rs28602964	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28768211	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930944	0.81[ASN][1000 genomes]
rs2930945	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930946	0.81[ASN][1000 genomes]
rs2930949	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930951	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932767	0.85[ASN][1000 genomes]
rs2932770	0.81[ASN][1000 genomes]
rs2932771	0.81[ASN][1000 genomes]
rs2932772	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932773	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932774	0.81[AMR][1000 genomes]
rs2932775	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932776	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932777	0.81[ASN][1000 genomes]
rs2932778	0.82[ASN][1000 genomes]
rs2932780	0.85[ASN][1000 genomes]
rs2932782	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932783	0.85[ASN][1000 genomes]
rs2972358	0.81[ASN][1000 genomes]
rs2972366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972373	0.81[ASN][1000 genomes]
rs2972374	0.81[ASN][1000 genomes]
rs2972377	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972378	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972381	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972386	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972387	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972388	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972390	0.81[ASN][1000 genomes]
rs34893396	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34935424	0.85[ASN][1000 genomes]
rs350104	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs350106	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs350107	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350109	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350115	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350116	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350122	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350123	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350124	0.81[ASN][1000 genomes]
rs351424	0.89[ASN][1000 genomes]
rs35308484	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs353656	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs379106	0.89[ASN][1000 genomes]
rs386640	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3934528	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077460	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419902	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs426392	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4266362	0.91[ASN][1000 genomes]
rs4362903	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4421064	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4541612	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4629549	0.92[ASN][1000 genomes]
rs488498	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4976188	0.80[ASN][1000 genomes]
rs4976189	0.85[ASN][1000 genomes]
rs603029	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62373164	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450026	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6450027	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6450029	0.85[ASN][1000 genomes]
rs651076	0.87[ASN][1000 genomes]
rs676012	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs676879	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6862253	0.83[ASN][1000 genomes]
rs6866993	0.92[ASN][1000 genomes]
rs6873869	0.85[ASN][1000 genomes]
rs6876783	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693725	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7733556	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1795469	chr5:68534233-68565285	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv965550	chr5:68556472-68572197	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3414951	chr5:68560228-68560711	Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2972361	CCDC125	cis	Muscle Skeletal	GTEx
rs2972361	CCDC125	cis	lung	GTEx
rs2972361	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2972361	GUSBP3	cis	Whole Blood	GTEx
rs2972361	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
4	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
5	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
7	chr5:68538400-68563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
9	chr5:68546200-68560600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:68546200-68562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr5:68546200-68579200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:68546400-68569000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:68546600-68566600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:68548400-68560600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:68548600-68566600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr5:68548800-68562000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:68549400-68565000	Weak transcription	Small Intestine	intestine
18	chr5:68549400-68577600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:68549600-68577600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:68549800-68567800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:68550400-68581800	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr5:68550600-68561000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:68550600-68562800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:68550600-68577000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:68550800-68566600	Strong transcription	HSMM	muscle
26	chr5:68550800-68568400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:68550800-68569600	Strong transcription	Primary B cells from cord blood	blood
28	chr5:68551200-68562000	Strong transcription	Placenta	Placenta
29	chr5:68551200-68567000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:68551400-68567400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:68551600-68560800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:68551600-68560800	Strong transcription	Fetal Intestine Large	intestine
33	chr5:68551600-68562000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:68551600-68562000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:68551600-68568000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr5:68551800-68562600	Strong transcription	Dnd41	blood
37	chr5:68551800-68568000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:68551800-68570200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:68552000-68562200	Strong transcription	Liver	Liver
40	chr5:68552000-68566200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:68552000-68566400	Strong transcription	Fetal Muscle Leg	muscle
42	chr5:68552000-68567000	Strong transcription	Primary T cells from cord blood	blood
43	chr5:68552000-68581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:68552200-68560600	Strong transcription	Brain Hippocampus Middle	brain
45	chr5:68552200-68560600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr5:68552200-68580800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:68552200-68588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:68552400-68566600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:68552600-68561000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:68553000-68560600	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links