Variant report

Variant	rs2450230
Chromosome Location	chr5:68511298-68511299
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	chr5:68511223-68511572	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:68510830-68511389	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68509300..68511885-chr5:68513443..68516137,3	K562	blood:

Variant related genes	Relation type
MRPS36	TF binding region
ENSG00000134056	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs100192	0.81[ASN][1000 genomes]
rs10063757	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10940209	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940210	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940212	0.83[ASN][1000 genomes]
rs10940216	0.83[ASN][1000 genomes]
rs11744596	0.84[ASN][1000 genomes]
rs11748974	0.90[ASN][1000 genomes]
rs12659146	0.84[ASN][1000 genomes]
rs13175606	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs151589	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163442	0.81[ASN][1000 genomes]
rs163443	0.81[ASN][1000 genomes]
rs163444	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164386	0.81[ASN][1000 genomes]
rs164388	0.81[ASN][1000 genomes]
rs164390	0.81[ASN][1000 genomes]
rs164709	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs164715	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164789	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1650779	0.90[ASN][1000 genomes]
rs171212	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs184747	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1976103	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2002825	0.84[ASN][1000 genomes]
rs2130757	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171148	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172056	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242350	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2242351	0.84[ASN][1000 genomes]
rs2291519	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291520	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450246	0.88[ASN][1000 genomes]
rs2637128	0.83[ASN][1000 genomes]
rs28602964	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28768211	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2930944	0.84[ASN][1000 genomes]
rs2930945	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2930946	0.84[ASN][1000 genomes]
rs2930949	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930951	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932767	0.88[ASN][1000 genomes]
rs2932770	0.84[ASN][1000 genomes]
rs2932771	0.84[ASN][1000 genomes]
rs2932772	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932773	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932774	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2932775	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932776	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932777	0.84[ASN][1000 genomes]
rs2932778	0.83[ASN][1000 genomes]
rs2932782	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972358	0.84[ASN][1000 genomes]
rs2972361	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972366	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972373	0.84[ASN][1000 genomes]
rs2972374	0.84[ASN][1000 genomes]
rs2972377	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972378	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972381	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972386	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972387	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972388	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972390	0.84[ASN][1000 genomes]
rs34845020	0.82[ASN][1000 genomes]
rs34893396	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34935424	0.86[ASN][1000 genomes]
rs350095	0.82[ASN][1000 genomes]
rs350099	0.81[ASN][1000 genomes]
rs350104	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs350106	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs350107	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350109	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350115	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350116	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350119	0.80[ASN][1000 genomes]
rs350120	0.81[ASN][1000 genomes]
rs350122	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350123	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350124	0.84[ASN][1000 genomes]
rs350125	0.83[ASN][1000 genomes]
rs351424	0.92[ASN][1000 genomes]
rs352626	0.81[ASN][1000 genomes]
rs35308484	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs353656	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs375285	0.81[ASN][1000 genomes]
rs376768	0.81[ASN][1000 genomes]
rs379106	0.92[ASN][1000 genomes]
rs379434	0.81[ASN][1000 genomes]
rs386640	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389938	0.81[ASN][1000 genomes]
rs3934528	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs395122	0.81[ASN][1000 genomes]
rs4077460	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs419902	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426392	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4266362	0.91[ASN][1000 genomes]
rs4362903	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4421064	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs444305	0.82[ASN][1000 genomes]
rs4541612	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4629549	0.93[ASN][1000 genomes]
rs488498	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4976189	0.85[ASN][1000 genomes]
rs603029	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62373164	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450026	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6450027	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6450029	0.86[ASN][1000 genomes]
rs648489	0.81[ASN][1000 genomes]
rs651076	0.90[ASN][1000 genomes]
rs676012	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs676879	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6866993	0.93[ASN][1000 genomes]
rs6873869	0.86[ASN][1000 genomes]
rs6876783	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693725	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7719040	0.81[ASN][1000 genomes]
rs7733556	0.93[ASN][1000 genomes]
rs875459	0.81[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2450230	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs2450230	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2450230	CCDC125	cis	lung	GTEx
rs2450230	GUSBP3	cis	Whole Blood	GTEx
rs2450230	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68513600	Weak transcription	Gastric	stomach
2	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
6	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
7	chr5:68486400-68513000	Weak transcription	Osteobl	bone
8	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:68492400-68513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:68492800-68512200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:68492800-68513000	Weak transcription	Fetal Brain Female	brain
12	chr5:68494600-68513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:68495400-68512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:68495400-68513000	Weak transcription	HMEC	breast
15	chr5:68495400-68513400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:68495600-68512400	Weak transcription	Primary T cells from cord blood	blood
17	chr5:68495600-68512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:68495600-68512800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr5:68495600-68513000	Weak transcription	Fetal Lung	lung
20	chr5:68495600-68513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr5:68495600-68513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:68497800-68513200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:68498000-68512800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:68500600-68513000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:68501600-68513000	Weak transcription	Thymus	Thymus
26	chr5:68502800-68513600	Weak transcription	Small Intestine	intestine
27	chr5:68505400-68513000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:68506400-68513000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:68507000-68513000	Weak transcription	Fetal Stomach	stomach
30	chr5:68507000-68513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:68507200-68513000	Weak transcription	Fetal Intestine Small	intestine
32	chr5:68507400-68512800	Weak transcription	Fetal Thymus	thymus
33	chr5:68507400-68513400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:68507600-68513000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:68507600-68513000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:68507600-68513000	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:68507600-68513200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:68507800-68512400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:68508000-68512000	Weak transcription	Dnd41	blood
40	chr5:68508000-68512800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:68508000-68513000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:68508000-68513200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:68508000-68513400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:68508000-68513400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:68508200-68512800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:68508200-68513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:68508200-68513000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:68508200-68513000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:68509600-68513000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:68509600-68513600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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