Variant report

Variant	rs35308484
Chromosome Location	chr5:68520544-68520545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10045526	0.84[ASN][1000 genomes]
rs10063757	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063969	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10940209	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10940210	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12513817	0.88[ASN][1000 genomes]
rs13175606	0.89[EUR][1000 genomes]
rs13362324	0.88[ASN][1000 genomes]
rs151589	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs163444	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs164709	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164715	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs164789	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171211	0.99[ASN][1000 genomes]
rs171212	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs184747	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1976103	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2130757	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2171148	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2172056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2242350	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291519	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2291520	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2450230	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28602964	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28768211	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2930945	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2930949	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2930951	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932772	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2932773	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2932774	0.82[EUR][1000 genomes]
rs2932775	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2932776	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932782	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2972361	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2972366	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2972377	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2972378	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2972381	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2972386	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2972387	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2972388	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34893396	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350104	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350106	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350107	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs350109	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs350115	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs350116	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs350122	0.90[EUR][1000 genomes]
rs350123	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs353656	0.87[EUR][1000 genomes]
rs386640	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3890705	0.87[ASN][1000 genomes]
rs3934528	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4077460	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs419902	0.93[EUR][1000 genomes]
rs426392	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4362903	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4421064	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs488498	0.92[EUR][1000 genomes]
rs60299793	0.80[ASN][1000 genomes]
rs603029	0.89[EUR][1000 genomes]
rs62373164	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62373181	0.82[ASN][1000 genomes]
rs6450026	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6450027	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs676012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676879	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6876783	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs693725	0.83[AMR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35308484	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs35308484	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs35308484	CCDC125	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68514200-68530200	Weak transcription	Small Intestine	intestine
2	chr5:68514200-68530200	Weak transcription	Spleen	Spleen
3	chr5:68514400-68521800	Weak transcription	Placenta	Placenta
4	chr5:68514400-68523000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:68514400-68523600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
11	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
12	chr5:68514400-68530200	Weak transcription	Gastric	stomach
13	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
14	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:68514600-68522200	Weak transcription	Fetal Thymus	thymus
16	chr5:68514600-68523000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:68514600-68523400	Weak transcription	HSMM	muscle
18	chr5:68514600-68523600	Weak transcription	Ovary	ovary
19	chr5:68514600-68524000	Weak transcription	HSMMtube	muscle
20	chr5:68514800-68521600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:68514800-68521600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:68514800-68521600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:68514800-68523000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:68514800-68523400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr5:68514800-68523400	Weak transcription	Osteobl	bone
26	chr5:68514800-68523600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:68514800-68524000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:68514800-68524000	Weak transcription	NH-A	brain
29	chr5:68514800-68524200	Weak transcription	HUVEC	blood vessel
30	chr5:68514800-68530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:68515000-68523000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:68515000-68523400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:68515000-68524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:68515000-68524200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:68515000-68530000	Weak transcription	Psoas Muscle	Psoas
36	chr5:68515200-68522800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:68515200-68523000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr5:68515200-68523000	Weak transcription	A549	lung
39	chr5:68515200-68523400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:68515200-68523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:68515200-68523400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:68515200-68523400	Weak transcription	Adipose Nuclei	Adipose
43	chr5:68515200-68523400	Weak transcription	NHEK	skin
44	chr5:68515200-68523600	Weak transcription	Primary T cells from cord blood	blood
45	chr5:68515200-68523600	Weak transcription	HMEC	breast
46	chr5:68515200-68524000	Weak transcription	Brain Germinal Matrix	brain
47	chr5:68515200-68524000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:68515200-68529800	Weak transcription	Fetal Brain Female	brain
49	chr5:68515200-68529800	Weak transcription	NHLF	lung
50	chr5:68515200-68530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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