Variant report

Variant	rs1976103
Chromosome Location	chr5:68496780-68496781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68496257..68497924-chr5:68621428..68624082,2	K562	blood:
2	chr5:68468383..68471229-chr5:68496445..68498720,2	K562	blood:
3	chr5:68496437..68498055-chr5:68501214..68502834,2	K562	blood:

Variant related genes	Relation type
ENSG00000134057	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10063757	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10940209	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10940210	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13175606	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs151589	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs163444	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs164709	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs164715	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs164789	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs171212	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs184747	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2130757	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2171148	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172056	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2242350	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2291519	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2291520	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2450230	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28602964	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28768211	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2930945	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2930949	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2930951	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2932772	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2932773	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2932774	0.81[EUR][1000 genomes]
rs2932775	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2932776	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2932782	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2972361	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2972366	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2972377	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2972378	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2972381	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2972386	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2972387	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2972388	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34893396	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350104	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350106	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs350107	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs350109	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs350115	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs350116	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs350122	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs350123	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35308484	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs353656	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs386640	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3934528	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4077460	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs419902	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs426392	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4362903	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4421064	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs488498	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs603029	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62373164	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6450026	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6450027	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs676012	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs676879	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6876783	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs693725	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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
rs1976103	CCDC125	cis	lung	GTEx
rs1976103	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs1976103	GUSBP3	cis	Whole Blood	GTEx
rs1976103	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68498200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:68486000-68498600	Weak transcription	Left Ventricle	heart
3	chr5:68486000-68505800	Weak transcription	Ovary	ovary
4	chr5:68486000-68513600	Weak transcription	Gastric	stomach
5	chr5:68486200-68497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:68486200-68497600	Weak transcription	Fetal Heart	heart
7	chr5:68486200-68497600	Weak transcription	Pancreas	Pancrea
8	chr5:68486200-68498200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:68486200-68498400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:68486200-68499200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:68486200-68499400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
13	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
14	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
16	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:68486200-68509400	Weak transcription	HSMM	muscle
20	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr5:68486400-68496800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:68486400-68502400	Weak transcription	NH-A	brain
23	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
24	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
25	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
26	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
28	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
29	chr5:68486400-68513000	Weak transcription	Osteobl	bone
30	chr5:68486600-68497200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:68486600-68502600	Weak transcription	NHLF	lung
32	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
33	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:68487600-68498000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:68487600-68500400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:68487600-68500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:68487600-68500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:68487600-68503000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr5:68487600-68503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:68487600-68508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:68487600-68508000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:68487600-68508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:68488200-68501600	Strong transcription	Dnd41	blood
46	chr5:68488400-68502200	Weak transcription	NHEK	skin
47	chr5:68488600-68507400	Weak transcription	GM12878-XiMat	blood
48	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr5:68490800-68501000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:68492200-68498400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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