Variant report

Variant	rs2972374
Chromosome Location	chr5:68514822-68514823
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68513358..68515252-chr5:68629266..68631706,2	K562	blood:
2	chr5:68471354..68475028-chr5:68512445..68515750,4	K562	blood:
3	chr5:68514007..68516074-chr5:68664468..68668135,3	K562	blood:
4	chr5:68484254..68487485-chr5:68512131..68515372,4	K562	blood:
5	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:
6	chr5:68461458..68463761-chr5:68512888..68515184,2	MCF-7	breast:
7	chr5:68388388..68391466-chr5:68512032..68515267,4	MCF-7	breast:
8	chr5:68514651..68516753-chr5:68670108..68672785,2	K562	blood:
9	chr5:68514182..68515689-chr5:68624413..68626099,2	MCF-7	breast:
10	chr5:68512209..68515422-chr5:68529314..68532677,7	MCF-7	breast:
11	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
12	chr5:68461057..68464340-chr5:68513596..68515366,3	K562	blood:
13	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:
14	chr5:68388860..68391967-chr5:68513712..68515652,4	K562	blood:
15	chr5:68513382..68515686-chr5:68665012..68667135,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215006	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000134057	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs100192	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940209	0.81[ASN][1000 genomes]
rs11742461	0.90[ASN][1000 genomes]
rs11744596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745578	0.90[ASN][1000 genomes]
rs11748974	0.80[ASN][1000 genomes]
rs12659146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175606	0.83[ASN][1000 genomes]
rs151589	0.83[ASN][1000 genomes]
rs163442	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs163443	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163444	0.83[ASN][1000 genomes]
rs164386	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164388	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164389	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164390	0.91[AMR][1000 genomes];0.89[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450230	0.84[ASN][1000 genomes]
rs2637128	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637129	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930945	0.85[ASN][1000 genomes]
rs2930946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930949	0.81[ASN][1000 genomes]
rs2930951	0.81[ASN][1000 genomes]
rs2932770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932771	0.94[AMR][1000 genomes];1.00[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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932782	0.80[ASN][1000 genomes]
rs2932783	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972358	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972361	0.81[ASN][1000 genomes]
rs2972366	0.81[ASN][1000 genomes]
rs2972373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
rs2972390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34845020	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350093	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350094	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350095	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350099	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350105	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350107	0.83[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.83[ASN][1000 genomes]
rs350119	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350120	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350123	0.85[ASN][1000 genomes]
rs350124	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs352626	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353656	0.82[ASN][1000 genomes]
rs375285	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376768	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379434	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs386640	0.83[ASN][1000 genomes]
rs389686	0.92[ASN][1000 genomes]
rs389938	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390169	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395122	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419902	0.83[ASN][1000 genomes]
rs4266362	0.82[ASN][1000 genomes]
rs437665	0.92[ASN][1000 genomes]
rs444305	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476125	0.92[ASN][1000 genomes]
rs4976159	0.91[ASN][1000 genomes]
rs4976188	0.91[ASN][1000 genomes]
rs648489	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651076	0.80[ASN][1000 genomes]
rs676879	0.81[ASN][1000 genomes]
rs6862253	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs693725	0.83[ASN][1000 genomes]
rs7719040	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875459	0.93[AMR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2972374	CCDC125	cis	Muscle Skeletal	GTEx
rs2972374	CDK7	cis	Muscle Skeletal	GTEx
rs2972374	MRPS36	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68512400-68515200	Active TSS	A549	lung
2	chr5:68512400-68515200	Active TSS	Hela-S3	cervix
3	chr5:68512800-68515200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:68513000-68515000	Active TSS	Psoas Muscle	Psoas
5	chr5:68513000-68515200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr5:68513000-68515200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:68513000-68515200	Active TSS	Fetal Kidney	kidney
8	chr5:68513000-68515200	Active TSS	Stomach Smooth Muscle	stomach
9	chr5:68513000-68515400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:68513200-68515200	Active TSS	Right Ventricle	heart
11	chr5:68513400-68515000	Active TSS	HMEC	breast
12	chr5:68513600-68515200	Active TSS	Left Ventricle	heart
13	chr5:68514000-68515400	Active TSS	Right Atrium	heart
14	chr5:68514200-68515000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:68514200-68515200	Flanking Active TSS	Dnd41	blood
16	chr5:68514200-68530200	Weak transcription	Small Intestine	intestine
17	chr5:68514200-68530200	Weak transcription	Spleen	Spleen
18	chr5:68514400-68515000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:68514400-68515000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:68514400-68515000	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr5:68514400-68515000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:68514400-68515000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:68514400-68515200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:68514400-68515200	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr5:68514400-68515400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr5:68514400-68515400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:68514400-68515400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr5:68514400-68515600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:68514400-68515600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:68514400-68515600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr5:68514400-68515600	Enhancers	Brain Substantia Nigra	brain
32	chr5:68514400-68515800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:68514400-68515800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr5:68514400-68520400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:68514400-68520400	Weak transcription	Lung	lung
36	chr5:68514400-68521800	Weak transcription	Placenta	Placenta
37	chr5:68514400-68523000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr5:68514400-68523600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
44	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
45	chr5:68514400-68530200	Weak transcription	Gastric	stomach
46	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
47	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr5:68514600-68515000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:68514600-68515000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr5:68514600-68515000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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