Variant report

Variant	rs426392
Chromosome Location	chr5:68470559-68470560
allele	A/G
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	chr5:68470550-68471107	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:68470524-68471446	K562	blood:	n/a	n/a
3	POLR2A	chr5:68470403-68471882	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CCNB1	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10045526	0.83[ASN][1000 genomes]
rs10063757	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10063969	0.98[ASN][1000 genomes]
rs10940209	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10940210	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12513817	0.87[ASN][1000 genomes]
rs13175606	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13362324	0.87[ASN][1000 genomes]
rs151589	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs163444	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs164709	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164715	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs164789	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171211	0.97[ASN][1000 genomes]
rs171212	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs184747	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1976103	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2130757	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2171148	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172056	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2242350	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291519	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2291520	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2450230	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28602964	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28768211	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2930945	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2930949	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2930951	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2932772	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932773	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932775	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932776	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2932782	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2972361	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2972366	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2972377	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2972378	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2972381	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2972386	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2972387	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2972388	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34893396	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350104	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350106	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350107	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs350109	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350115	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs350116	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350122	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs350123	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35308484	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs353656	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs386640	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3890705	0.86[ASN][1000 genomes]
rs419902	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4362903	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs488498	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs603029	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62373181	0.80[ASN][1000 genomes]
rs6450026	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6450027	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs676012	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs676879	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6876783	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs693725	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

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	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs426392	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs426392	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs426392	CCDC125	cis	Muscle Skeletal	GTEx
rs426392	CCDC125	cis	lung	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68463800-68470800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:68463800-68484400	Weak transcription	Adipose Nuclei	Adipose
3	chr5:68463800-68484400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:68463800-68484400	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:68464000-68470800	Weak transcription	Liver	Liver
6	chr5:68464000-68470800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:68464000-68471000	Weak transcription	Brain Angular Gyrus	brain
8	chr5:68464000-68472800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:68464000-68473000	Weak transcription	Esophagus	oesophagus
10	chr5:68464000-68473400	Weak transcription	Fetal Brain Male	brain
11	chr5:68464000-68475000	Weak transcription	Colonic Mucosa	Colon
12	chr5:68464000-68476200	Weak transcription	Stomach Mucosa	stomach
13	chr5:68464000-68478000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:68464000-68478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:68464000-68484400	Weak transcription	Pancreas	Pancrea
16	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
17	chr5:68464200-68470800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:68464200-68470800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:68464200-68471000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:68464200-68474000	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr5:68464200-68474000	Weak transcription	Small Intestine	intestine
22	chr5:68464200-68474600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
24	chr5:68464400-68470600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:68464400-68470800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:68464400-68471000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:68464400-68473200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:68464400-68473200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:68464400-68473600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:68464600-68470800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:68464600-68473600	Strong transcription	Fetal Muscle Leg	muscle
34	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
35	chr5:68464800-68474000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:68464800-68474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:68464800-68474400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:68464800-68474600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:68464800-68474600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr5:68464800-68474600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:68464800-68474600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:68465000-68473800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:68465200-68473000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:68465200-68474600	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr5:68465400-68471400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:68465400-68471600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:68465400-68474000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:68465400-68474400	Strong transcription	HSMM	muscle
49	chr5:68465400-68474800	Strong transcription	NHEK	skin
50	chr5:68465600-68474800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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