Variant report

Variant	rs2291519
Chromosome Location	chr5:68551507-68551508
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68530371..68532104-chr5:68550498..68552511,2	MCF-7	breast:
2	chr5:68549479..68552120-chr5:68553320..68555643,3	K562	blood:
3	chr5:68529657..68532330-chr5:68550673..68553166,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS36-2	chr5:68551287-68551848	NONHSAT101904

Variant related genes	Relation type
ENSG00000134058	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs100192	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs10063757	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10940209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940210	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13362324	0.81[EUR][1000 genomes]
rs151589	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs163443	0.91[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs163444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164386	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs164390	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs164709	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs164715	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164789	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1650779	0.87[ASN][1000 genomes]
rs171212	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs184747	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1976103	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2002825	0.81[ASN][1000 genomes]
rs2130757	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171148	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2172056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242350	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2242351	0.81[ASN][1000 genomes]
rs2291520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450230	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450246	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2637128	0.80[ASN][1000 genomes]
rs28602964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28768211	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930944	0.81[ASN][1000 genomes]
rs2930945	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930946	0.81[ASN][1000 genomes]
rs2930949	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930951	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932773	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932774	0.81[AMR][1000 genomes]
rs2932775	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932776	0.96[AMR][1000 genomes];0.92[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	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932783	0.85[ASN][1000 genomes]
rs2972358	0.81[ASN][1000 genomes]
rs2972361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972378	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972381	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972386	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972387	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972388	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972390	0.81[ASN][1000 genomes]
rs34893396	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34935424	0.85[ASN][1000 genomes]
rs350104	0.80[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs350106	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350107	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350109	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350115	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350116	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350122	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs350123	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350124	0.81[ASN][1000 genomes]
rs351424	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.89[ASN][1000 genomes]
rs352626	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs35308484	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs353656	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs379106	0.89[ASN][1000 genomes]
rs386640	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3890705	0.81[EUR][1000 genomes]
rs389686	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs3934528	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077460	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419902	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs426392	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4266362	0.91[ASN][1000 genomes]
rs4362903	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437665	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4421064	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs444305	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4541612	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4629549	0.92[ASN][1000 genomes]
rs488498	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4976188	0.80[ASN][1000 genomes]
rs4976189	0.85[ASN][1000 genomes]
rs603029	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62373164	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6450026	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6450027	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6450029	0.85[ASN][1000 genomes]
rs648489	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs651076	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs676012	1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs676879	0.97[AMR][1000 genomes];0.93[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	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs693725	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7733556	0.92[ASN][1000 genomes]
rs875459	0.91[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2291519	CCDC125	cis	lung	GTEx
rs2291519	GUSBP3	cis	Whole Blood	GTEx
rs2291519	MRPS36	cis	multi-tissue	Pritchard
rs2291519	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2291519	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2291519	CCDC125	cis	Muscle Skeletal	GTEx
rs2291519	MRPS36	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 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	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:68531800-68552200	Weak transcription	Colonic Mucosa	Colon
5	chr5:68531800-68552200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:68531800-68554600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:68531800-68556000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:68531800-68556800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:68532200-68553400	Weak transcription	Fetal Heart	heart
10	chr5:68532400-68551600	Weak transcription	Ovary	ovary
11	chr5:68532400-68558600	Weak transcription	Brain Substantia Nigra	brain
12	chr5:68532400-68558800	Weak transcription	Brain Angular Gyrus	brain
13	chr5:68532400-68563600	Weak transcription	Fetal Brain Male	brain
14	chr5:68532400-68574600	Weak transcription	Spleen	Spleen
15	chr5:68533200-68576800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:68533600-68552200	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:68533600-68552400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:68534200-68552400	Weak transcription	Fetal Brain Female	brain
19	chr5:68534400-68552000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr5:68534400-68554600	Weak transcription	Gastric	stomach
21	chr5:68534400-68556000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr5:68534400-68575200	Weak transcription	Aorta	Aorta
23	chr5:68534800-68551800	Weak transcription	Left Ventricle	heart
24	chr5:68534800-68554200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:68535000-68551600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:68535200-68558800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:68535200-68559400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:68535400-68551600	Weak transcription	HUVEC	blood vessel
29	chr5:68535400-68553400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:68535400-68553400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:68535400-68556600	Weak transcription	HSMMtube	muscle
32	chr5:68535600-68552400	Weak transcription	Fetal Kidney	kidney
33	chr5:68536400-68552600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:68536600-68551600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:68536600-68551600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:68536800-68551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:68536800-68553000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr5:68537000-68551600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:68537000-68551800	Weak transcription	Dnd41	blood
40	chr5:68538400-68552000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:68538400-68552600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:68538400-68563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:68538600-68552400	Weak transcription	NH-A	brain
44	chr5:68538800-68553400	Weak transcription	NHLF	lung
45	chr5:68539000-68559200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:68539200-68554600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
48	chr5:68544600-68554600	Weak transcription	Brain Germinal Matrix	brain
49	chr5:68545000-68551600	Weak transcription	Fetal Intestine Large	intestine
50	chr5:68545200-68552200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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