Variant report

Variant	rs350099
Chromosome Location	chr5:68461956-68461957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68461951-68464229	GM12891	blood:	n/a	n/a
2	RFX5	chr5:68461829-68464062	SK-N-SH	brain:	n/a	chr5:68463363-68463379
3	MXI1	chr5:68461948-68464340	IMR90	lung:	n/a	chr5:68462851-68462866

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:68461940-68461990	HNPCEpiC	eye:	n/a
2	chr5:68461940-68461990	HL-60	blood:	n/a
3	chr5:68461940-68461990	HEK293	kidney:	embryo
4	chr5:68461940-68461990	ovcar-3	ovarian:	n/a
5	chr5:68461940-68461990	HRPEpiC	eye:	n/a
6	chr5:68461940-68461990	HCPEpiC	choroid plexus:	n/a
7	chr5:68461940-68461990	BJ	skin:	n/a
8	chr5:68461940-68461990	SAEC	small airway:	n/a
9	chr5:68461940-68461990	AG09319	gingival:	n/a
10	chr5:68461940-68461990	Jurkat	blood:	n/a
11	chr5:68461940-68461990	ProgFib	skin:	n/a
12	chr5:68461940-68461990	Hela-S3	cervix:	n/a
13	chr5:68461940-68461990	HAEpiC	amniotic membrane:	n/a
14	chr5:68461940-68461990	GM12891	blood:	n/a
15	chr5:68461940-68461990	HRE	kidney:	n/a
16	chr5:68461940-68461990	U87	brain:	n/a
17	chr5:68461940-68461990	PrEC	prostate:	n/a
18	chr5:68461940-68461990	SKMC	muscle:	n/a
19	chr5:68461940-68461990	HCT-116	colon:	n/a
20	chr5:68461940-68461990	SK-N-MC	brain:	n/a
21	chr5:68461940-68461990	HCM	heart:	n/a
22	chr5:68461940-68461990	H1-hESC	embryonic stem cell:	embryo
23	chr5:68461940-68461990	NHDF-neo	bronchial:	n/a
24	chr5:68461940-68461990	A549	lung:	n/a
25	chr5:68461940-68461990	Caco-2	colon:	n/a
26	chr5:68461940-68461990	BE2_C	brain:	n/a
27	chr5:68461940-68461990	SK-N-SH_RA	brain:	n/a
28	chr5:68461940-68461990	HepG2	liver:	n/a
29	chr5:68461940-68461990	MCF-7	breast:	n/a
30	chr5:68461940-68461990	NT2-D1	testis:	n/a
31	chr5:68461940-68461990	PANC-1	pancreas:	n/a
32	chr5:68461940-68461990	NHBE	bronchial:	n/a
33	chr5:68461940-68461990	AG04450	lung:	fetal
34	chr5:68461940-68461990	HPAEpiC	pulmonary alveolar:	n/a
35	chr5:68461940-68461990	CMK	blood:	n/a
36	chr5:68461940-68461990	ECC-1	luminal epithelium:	n/a
37	chr5:68461940-68461990	RPTEC	kidney:	n/a
38	chr5:68461940-68461990	LNCaP	prostate:	n/a
39	chr5:68461940-68461990	GM12878	blood:	n/a
40	chr5:68461940-68461990	AG04449	skin:	fetal
41	chr5:68461940-68461990	HRCEpiC	kidney:	n/a
42	chr5:68461940-68461990	GM12892	blood:	n/a
43	chr5:68461940-68461990	NB4	blood:	n/a
44	chr5:68461940-68461990	HIPEpiC	eye:	n/a
45	chr5:68461940-68461990	GM19239	blood:	n/a
46	chr5:68461940-68461990	PFSK-1	brain:	n/a
47	chr5:68461940-68461990	AG10803	skin:	n/a
48	chr5:68461940-68461990	NH-A	brain:	n/a
49	chr5:68461940-68461990	AoSMC	blood vessel:	n/a
50	chr5:68461940-68461990	SK-N-SH	brain:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68461458..68463761-chr5:68512888..68515184,2	MCF-7	breast:
2	chr5:68452033..68456569-chr5:68461553..68463610,4	K562	blood:
3	chr5:68461460..68464018-chr5:68483608..68486992,6	MCF-7	breast:
4	chr5:68461677..68464671-chr5:68665186..68667008,2	MCF-7	breast:
5	chr5:68461899..68464283-chr5:68662357..68663862,2	K562	blood:
6	chr5:68461057..68464340-chr5:68513596..68515366,3	K562	blood:
7	chr5:68461424..68464982-chr5:68663773..68666998,5	K562	blood:
8	chr5:68387785..68391337-chr5:68461261..68464730,5	K562	blood:

No data

Variant related genes	Relation type
CCNB1	TF binding region
CCNB1	CpG island
ENSG00000134056	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000265968	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs100192	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11742461	0.85[ASN][1000 genomes]
rs11744596	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11745578	0.85[ASN][1000 genomes]
rs12659146	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13175606	0.85[ASN][1000 genomes]
rs151589	0.85[ASN][1000 genomes]
rs163442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs163444	0.85[ASN][1000 genomes]
rs164386	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164388	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164389	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164390	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164715	0.85[ASN][1000 genomes]
rs1650779	0.81[ASN][1000 genomes]
rs1683831	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs184747	0.85[ASN][1000 genomes]
rs2002825	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242351	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239591	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2450230	0.81[ASN][1000 genomes]
rs2450246	0.80[ASN][1000 genomes]
rs2637128	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2637129	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28506805	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28576332	0.85[ASN][1000 genomes]
rs28693971	0.85[ASN][1000 genomes]
rs2913707	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2930944	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930945	0.82[ASN][1000 genomes]
rs2930946	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932767	0.80[ASN][1000 genomes]
rs2932770	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932771	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932772	0.83[ASN][1000 genomes]
rs2932773	0.83[ASN][1000 genomes]
rs2932775	0.83[ASN][1000 genomes]
rs2932776	0.83[ASN][1000 genomes]
rs2932777	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932778	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932780	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932783	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972358	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972373	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972374	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972390	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34845020	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350093	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350094	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs350095	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350105	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350107	0.85[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.85[ASN][1000 genomes]
rs350119	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350120	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350123	0.83[ASN][1000 genomes]
rs350124	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350125	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs351424	0.81[ASN][1000 genomes]
rs352626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353656	0.84[ASN][1000 genomes]
rs375285	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376768	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs379106	0.81[ASN][1000 genomes]
rs379434	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386640	0.85[ASN][1000 genomes]
rs389686	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs389938	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs390169	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs395122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419902	0.85[ASN][1000 genomes]
rs437665	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs444305	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476125	0.96[ASN][1000 genomes]
rs4976159	0.86[ASN][1000 genomes]
rs4976188	0.86[ASN][1000 genomes]
rs648489	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651076	0.82[ASN][1000 genomes]
rs6862253	0.84[ASN][1000 genomes]
rs693725	0.85[ASN][1000 genomes]
rs7719040	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875459	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs350099	CCDC125	cis	Muscle Skeletal	GTEx
rs350099	CDK7	cis	Muscle Skeletal	GTEx
rs350099	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68443600-68462000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:68453800-68462000	Weak transcription	K562	blood
3	chr5:68459400-68462400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:68461600-68464000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:68461800-68462000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:68461800-68462000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr5:68461800-68462000	Enhancers	Adipose Nuclei	Adipose
8	chr5:68461800-68462000	Enhancers	Brain Cingulate Gyrus	brain
9	chr5:68461800-68462200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:68461800-68462200	Enhancers	HepG2	liver
11	chr5:68461800-68462400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:68461800-68462400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr5:68461800-68462400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:68461800-68462400	Enhancers	Right Atrium	heart
15	chr5:68461800-68462600	Enhancers	Lung	lung
16	chr5:68461800-68462600	Enhancers	Pancreas	Pancrea
17	chr5:68461800-68462800	Flanking Active TSS	Dnd41	blood

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