Variant report

Variant	rs2972357
Chromosome Location	chr5:68528843-68528844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68528497-68528878	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:68527202-68531006	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68483901..68487830-chr5:68528757..68532922,9	K562	blood:
2	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:
3	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
4	chr5:68484558..68486629-chr5:68528757..68530623,2	K562	blood:
5	chr5:68527870..68529921-chr5:68647388..68650083,2	K562	blood:
6	chr5:68524400..68526328-chr5:68527569..68529446,2	K562	blood:

No data

Variant related genes	Relation type
CDK7	TF binding region
ENSG00000134056	Chromatin interaction
ENSG00000153044	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10805428	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134774	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11739602	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11741775	0.83[ASN][1000 genomes]
rs11741826	0.83[ASN][1000 genomes]
rs11742878	0.84[ASN][1000 genomes]
rs11745537	0.84[ASN][1000 genomes]
rs11745591	0.84[ASN][1000 genomes]
rs11951414	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs11952883	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs12188270	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12520485	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13161541	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13163459	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13178023	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13182409	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs163443	0.81[CHB][hapmap]
rs1976101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2054974	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054975	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054976	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2130756	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172055	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2327638	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2327639	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28499200	0.83[ASN][1000 genomes]
rs2932785	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932787	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932788	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932789	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932790	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932793	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972364	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972367	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972369	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2972379	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972384	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2972385	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34261117	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34449359	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34591347	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34657177	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350096	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350118	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350121	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4288083	0.80[ASN][1000 genomes]
rs4367248	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4423955	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62373182	0.84[ASN][1000 genomes]
rs668139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6865178	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6869305	0.80[ASN][1000 genomes]
rs71622283	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72767881	0.84[ASN][1000 genomes]
rs7706902	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7711657	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs875459	0.80[CEU][hapmap];0.81[CHB][hapmap]

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
rs2972357	RAD17	cis	Muscle Skeletal	GTEx
rs2972357	MRPS36	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 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	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
8	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
9	chr5:68514400-68530200	Weak transcription	Gastric	stomach
10	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
11	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:68514800-68530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:68515000-68530000	Weak transcription	Psoas Muscle	Psoas
14	chr5:68515200-68529800	Weak transcription	Fetal Brain Female	brain
15	chr5:68515200-68529800	Weak transcription	NHLF	lung
16	chr5:68515200-68530000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:68515200-68530000	Weak transcription	Fetal Brain Male	brain
18	chr5:68515200-68530000	Weak transcription	Fetal Kidney	kidney
19	chr5:68515200-68530000	Weak transcription	Fetal Lung	lung
20	chr5:68515400-68529400	Weak transcription	Fetal Heart	heart
21	chr5:68515400-68529800	Weak transcription	Brain Anterior Caudate	brain
22	chr5:68515400-68529800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:68515400-68529800	Weak transcription	Hela-S3	cervix
24	chr5:68515400-68530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:68515400-68530000	Weak transcription	Right Ventricle	heart
26	chr5:68515600-68530000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:68515600-68530000	Weak transcription	Brain Substantia Nigra	brain
28	chr5:68515800-68530000	Weak transcription	Brain Angular Gyrus	brain
29	chr5:68520800-68529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:68520800-68530200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:68521800-68530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:68523000-68530200	Weak transcription	Lung	lung
33	chr5:68523800-68530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:68524200-68529800	Weak transcription	Colonic Mucosa	Colon
35	chr5:68524400-68529600	Weak transcription	HSMMtube	muscle
36	chr5:68524400-68530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:68524400-68530000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:68524400-68530000	Weak transcription	HMEC	breast
39	chr5:68524400-68530200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr5:68524400-68530200	Weak transcription	Ovary	ovary
41	chr5:68524600-68529600	Weak transcription	Brain Germinal Matrix	brain
42	chr5:68524600-68529800	Weak transcription	Primary B cells from cord blood	blood
43	chr5:68524600-68529800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:68524600-68529800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:68524600-68529800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:68524600-68529800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr5:68524600-68529800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr5:68524600-68529800	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:68524600-68529800	Weak transcription	HepG2	liver
50	chr5:68524600-68529800	Weak transcription	HUVEC	blood vessel

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