Variant report

Variant	rs2972390
Chromosome Location	chr5:68529783-68529784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
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	RCOR1	chr5:68529725-68529936	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:68527202-68531006	K562	blood:	n/a	n/a
3	GATA1	chr5:68529699-68531162	PBDE	blood:	n/a	chr5:68530961-68530969

No data

(count:8 , 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	chr5:68529171..68532388-chr5:68663415..68666737,3	K562	blood:
4	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
5	chr5:68484558..68486629-chr5:68528757..68530623,2	K562	blood:
6	chr5:68527870..68529921-chr5:68647388..68650083,2	K562	blood:
7	chr5:68512209..68515422-chr5:68529314..68532677,7	MCF-7	breast:
8	chr5:68529081..68531056-chr5:68663452..68665244,2	MCF-7	breast:

No data

Variant related genes	Relation type
CDK7	TF binding region
ENSG00000134056	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs100192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940209	0.81[ASN][1000 genomes]
rs11742461	0.90[ASN][1000 genomes]
rs11744596	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745578	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748974	0.80[ASN][1000 genomes]
rs12659146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175606	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs151589	0.83[ASN][1000 genomes]
rs163442	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs163443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163444	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs164386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164388	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164389	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164715	0.83[ASN][1000 genomes]
rs1683831	0.92[ASN][1000 genomes]
rs184747	0.83[ASN][1000 genomes]
rs2002825	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2130757	0.81[ASN][1000 genomes]
rs2171148	0.81[ASN][1000 genomes]
rs2172056	0.81[ASN][1000 genomes]
rs2242351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291519	0.81[ASN][1000 genomes]
rs2291520	0.81[ASN][1000 genomes]
rs239591	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450230	0.84[ASN][1000 genomes]
rs2450246	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2637128	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637129	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28506805	0.92[ASN][1000 genomes]
rs28576332	0.90[ASN][1000 genomes]
rs28693971	0.90[ASN][1000 genomes]
rs2913707	0.83[ASN][1000 genomes]
rs2930944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930945	0.85[ASN][1000 genomes]
rs2930946	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930949	0.81[ASN][1000 genomes]
rs2930951	0.81[ASN][1000 genomes]
rs2932770	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932771	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932772	0.85[ASN][1000 genomes]
rs2932773	0.85[ASN][1000 genomes]
rs2932775	0.85[ASN][1000 genomes]
rs2932776	0.85[ASN][1000 genomes]
rs2932777	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932778	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932782	0.80[ASN][1000 genomes]
rs2932783	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972358	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972361	0.81[ASN][1000 genomes]
rs2972366	0.81[ASN][1000 genomes]
rs2972373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972374	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972381	0.81[ASN][1000 genomes]
rs2972386	0.81[ASN][1000 genomes]
rs2972387	0.81[ASN][1000 genomes]
rs2972388	0.80[ASN][1000 genomes]
rs34845020	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350093	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350094	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs350095	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350099	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350105	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350107	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.83[ASN][1000 genomes]
rs350119	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350120	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350123	0.85[ASN][1000 genomes]
rs350124	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350125	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351424	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs352626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353656	0.82[ASN][1000 genomes]
rs375285	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376768	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379434	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs386640	0.83[ASN][1000 genomes]
rs389686	0.88[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs389938	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390169	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395122	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419902	0.83[ASN][1000 genomes]
rs4266362	0.82[ASN][1000 genomes]
rs437665	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs444305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476125	0.92[ASN][1000 genomes]
rs4976159	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4976188	0.91[ASN][1000 genomes]
rs648489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651076	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs676879	0.81[ASN][1000 genomes]
rs6862253	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs693725	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7719040	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2972390	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2972390	MRPS36	cis	lymphoblastoid	seeQTL
rs2972390	CDK7	cis	Muscle Skeletal	GTEx
rs2972390	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 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	chr5:68515400-68529800	Weak transcription	Brain Anterior Caudate	brain
21	chr5:68515400-68529800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:68515400-68529800	Weak transcription	Hela-S3	cervix
23	chr5:68515400-68530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:68515400-68530000	Weak transcription	Right Ventricle	heart
25	chr5:68515600-68530000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:68515600-68530000	Weak transcription	Brain Substantia Nigra	brain
27	chr5:68515800-68530000	Weak transcription	Brain Angular Gyrus	brain
28	chr5:68520800-68529800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:68520800-68530200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:68521800-68530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:68523000-68530200	Weak transcription	Lung	lung
32	chr5:68523800-68530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:68524200-68529800	Weak transcription	Colonic Mucosa	Colon
34	chr5:68524400-68530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr5:68524400-68530000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:68524400-68530000	Weak transcription	HMEC	breast
37	chr5:68524400-68530200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:68524400-68530200	Weak transcription	Ovary	ovary
39	chr5:68524600-68529800	Weak transcription	Primary B cells from cord blood	blood
40	chr5:68524600-68529800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:68524600-68529800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:68524600-68529800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr5:68524600-68529800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:68524600-68529800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:68524600-68529800	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:68524600-68529800	Weak transcription	HepG2	liver
47	chr5:68524600-68529800	Weak transcription	HUVEC	blood vessel
48	chr5:68524600-68529800	Weak transcription	Osteobl	bone
49	chr5:68524600-68530000	Weak transcription	Primary T cells from cord blood	blood
50	chr5:68524600-68530000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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