Variant report

Variant	rs350109
Chromosome Location	chr5:68499499-68499500
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs100192	0.84[ASN][1000 genomes]
rs10063757	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10940209	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940210	0.92[AMR][1000 genomes];0.86[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	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151589	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs163442	0.84[ASN][1000 genomes]
rs163443	0.84[ASN][1000 genomes]
rs163444	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164386	0.84[ASN][1000 genomes]
rs164388	0.84[ASN][1000 genomes]
rs164389	0.82[ASN][1000 genomes]
rs164390	0.84[ASN][1000 genomes]
rs164709	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs164715	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164789	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1650779	0.93[ASN][1000 genomes]
rs1683831	0.80[ASN][1000 genomes]
rs171212	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs184747	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1976103	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2002825	0.84[ASN][1000 genomes]
rs2130757	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171148	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172056	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242350	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2242351	0.84[ASN][1000 genomes]
rs2291519	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291520	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2450230	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2450246	0.91[ASN][1000 genomes]
rs2637128	0.83[ASN][1000 genomes]
rs28506805	0.80[ASN][1000 genomes]
rs28602964	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28768211	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2930944	0.84[ASN][1000 genomes]
rs2930945	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2930946	0.84[ASN][1000 genomes]
rs2930949	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930951	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932767	0.91[ASN][1000 genomes]
rs2932770	0.84[ASN][1000 genomes]
rs2932771	0.84[ASN][1000 genomes]
rs2932772	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932773	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932774	0.81[EUR][1000 genomes]
rs2932775	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932776	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932777	0.84[ASN][1000 genomes]
rs2932778	0.83[ASN][1000 genomes]
rs2932782	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972358	0.84[ASN][1000 genomes]
rs2972361	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972366	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972373	0.84[ASN][1000 genomes]
rs2972374	0.84[ASN][1000 genomes]
rs2972377	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972378	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2972381	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972386	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972387	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972388	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972390	0.84[ASN][1000 genomes]
rs34845020	0.82[ASN][1000 genomes]
rs34893396	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34935424	0.86[ASN][1000 genomes]
rs350095	0.83[ASN][1000 genomes]
rs350099	0.84[ASN][1000 genomes]
rs350104	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350105	0.80[ASN][1000 genomes]
rs350106	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350107	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350115	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350116	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350119	0.83[ASN][1000 genomes]
rs350120	0.84[ASN][1000 genomes]
rs350122	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350123	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350124	0.84[ASN][1000 genomes]
rs350125	0.83[ASN][1000 genomes]
rs351424	0.94[ASN][1000 genomes]
rs352626	0.84[ASN][1000 genomes]
rs35308484	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353656	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs375285	0.84[ASN][1000 genomes]
rs376768	0.84[ASN][1000 genomes]
rs379106	0.94[ASN][1000 genomes]
rs379434	0.84[ASN][1000 genomes]
rs386640	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs389686	0.80[ASN][1000 genomes]
rs389938	0.84[ASN][1000 genomes]
rs3934528	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs395122	0.84[ASN][1000 genomes]
rs4077460	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs419902	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs426392	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4266362	0.91[ASN][1000 genomes]
rs4362903	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs437665	0.80[ASN][1000 genomes]
rs4421064	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs444305	0.85[ASN][1000 genomes]
rs4541612	0.90[ASN][1000 genomes]
rs4629549	0.93[ASN][1000 genomes]
rs476125	0.80[ASN][1000 genomes]
rs488498	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4976189	0.85[ASN][1000 genomes]
rs603029	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62373164	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450026	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6450027	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6450029	0.86[ASN][1000 genomes]
rs648489	0.84[ASN][1000 genomes]
rs651076	0.92[ASN][1000 genomes]
rs676012	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676879	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6866993	0.93[ASN][1000 genomes]
rs6873869	0.86[ASN][1000 genomes]
rs6876783	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs693725	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7719040	0.84[ASN][1000 genomes]
rs7733556	0.93[ASN][1000 genomes]
rs875459	0.84[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
rs350109	CCDC125	cis	Muscle Skeletal	GTEx
rs350109	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs350109	GUSBP3	cis	Whole Blood	GTEx
rs350109	CCDC125	cis	lung	GTEx
rs350109	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68505800	Weak transcription	Ovary	ovary
2	chr5:68486000-68513600	Weak transcription	Gastric	stomach
3	chr5:68486200-68500200	Weak transcription	Thymus	Thymus
4	chr5:68486200-68502000	Weak transcription	Placenta	Placenta
5	chr5:68486200-68502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
7	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:68486200-68509400	Weak transcription	HSMM	muscle
11	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:68486400-68502400	Weak transcription	NH-A	brain
13	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
14	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
15	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
16	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
18	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
19	chr5:68486400-68513000	Weak transcription	Osteobl	bone
20	chr5:68486600-68502600	Weak transcription	NHLF	lung
21	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
22	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:68487600-68500400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:68487600-68500400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:68487600-68500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:68487600-68503000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr5:68487600-68503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:68487600-68508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:68487600-68508000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:68487600-68508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:68488200-68501600	Strong transcription	Dnd41	blood
34	chr5:68488400-68502200	Weak transcription	NHEK	skin
35	chr5:68488600-68507400	Weak transcription	GM12878-XiMat	blood
36	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr5:68490800-68501000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:68492200-68501200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:68492400-68500000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr5:68492400-68504200	Weak transcription	Fetal Intestine Small	intestine
41	chr5:68492400-68504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:68492400-68513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:68492800-68512200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:68492800-68513000	Weak transcription	Fetal Brain Female	brain
45	chr5:68493000-68502400	Weak transcription	Hela-S3	cervix
46	chr5:68494000-68499800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:68494200-68509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:68494600-68513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:68495000-68505400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:68495000-68509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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