Variant report

Variant	rs350093
Chromosome Location	chr5:68502297-68502298
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	chr5:68502223-68502302	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68496437..68498055-chr5:68501214..68502834,2	K562	blood:

Variant related genes	Relation type
CENPH	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs100192	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11742461	0.83[ASN][1000 genomes]
rs11744596	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11745578	0.83[ASN][1000 genomes]
rs12659146	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs163442	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs163443	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164386	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164388	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164389	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164390	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1683831	0.85[ASN][1000 genomes]
rs2002825	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242351	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239591	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2637128	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2637129	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28506805	0.85[ASN][1000 genomes]
rs28576332	0.83[ASN][1000 genomes]
rs28693971	0.83[ASN][1000 genomes]
rs2930944	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2930946	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932770	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932771	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932777	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932778	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2932780	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2932783	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2972358	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972373	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972374	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972390	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34845020	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350094	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs350095	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350099	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350105	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs350119	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350120	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350124	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350125	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs352626	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs375285	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs376768	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs379434	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs389686	0.85[ASN][1000 genomes]
rs389938	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390169	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs395122	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs437665	0.85[ASN][1000 genomes]
rs444305	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476125	0.85[ASN][1000 genomes]
rs4976159	0.85[ASN][1000 genomes]
rs4976188	0.85[ASN][1000 genomes]
rs648489	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs676879	0.83[ASN][1000 genomes]
rs6862253	0.83[ASN][1000 genomes]
rs7719040	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875459	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs350093	CCDC125	cis	Muscle Skeletal	GTEx
rs350093	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 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	chr5:68486200-68502600	Weak transcription	Small Intestine	intestine
4	chr5:68486200-68505200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:68486200-68509400	Weak transcription	HSMM	muscle
8	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr5:68486400-68502400	Weak transcription	NH-A	brain
10	chr5:68486400-68502600	Weak transcription	Fetal Kidney	kidney
11	chr5:68486400-68502600	Weak transcription	HUVEC	blood vessel
12	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
13	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
15	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
16	chr5:68486400-68513000	Weak transcription	Osteobl	bone
17	chr5:68486600-68502600	Weak transcription	NHLF	lung
18	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
19	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:68487600-68503000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr5:68487600-68503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:68487600-68508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:68487600-68508000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:68487600-68508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:68488600-68507400	Weak transcription	GM12878-XiMat	blood
28	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:68492400-68504200	Weak transcription	Fetal Intestine Small	intestine
30	chr5:68492400-68504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:68492400-68513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:68492800-68512200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr5:68492800-68513000	Weak transcription	Fetal Brain Female	brain
34	chr5:68493000-68502400	Weak transcription	Hela-S3	cervix
35	chr5:68494200-68509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:68494600-68513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:68495000-68505400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:68495000-68509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:68495400-68512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:68495400-68513000	Weak transcription	HMEC	breast
41	chr5:68495400-68513400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:68495600-68509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:68495600-68512400	Weak transcription	Primary T cells from cord blood	blood
44	chr5:68495600-68512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:68495600-68512800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:68495600-68513000	Weak transcription	Fetal Lung	lung
47	chr5:68495600-68513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:68495600-68513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:68496200-68502400	Weak transcription	Right Atrium	heart
50	chr5:68497200-68506400	Weak transcription	Fetal Muscle Leg	muscle

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