Variant report

Variant	rs2930944
Chromosome Location	chr5:68515833-68515834
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68514007..68516074-chr5:68664468..68668135,3	K562	blood:
2	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:
3	chr5:68514651..68516753-chr5:68670108..68672785,2	K562	blood:
4	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
5	chr5:68514852..68516852-chr5:68553089..68555836,2	K562	blood:
6	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:

Variant related genes	Relation type
ENSG00000153044	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000134058	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]
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]
rs2972374	1.00[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
rs2930944	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2930944	CDK7	cis	Muscle Skeletal	GTEx
rs2930944	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:118 , 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	chr5:68514400-68520400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:68514400-68520400	Weak transcription	Lung	lung
5	chr5:68514400-68521800	Weak transcription	Placenta	Placenta
6	chr5:68514400-68523000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:68514400-68523600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:68514400-68530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:68514400-68530200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:68514400-68530200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:68514400-68530200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:68514400-68530200	Weak transcription	Aorta	Aorta
13	chr5:68514400-68530200	Weak transcription	Esophagus	oesophagus
14	chr5:68514400-68530200	Weak transcription	Gastric	stomach
15	chr5:68514400-68530200	Weak transcription	Pancreas	Pancrea
16	chr5:68514400-68530200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:68514600-68516000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:68514600-68520000	Weak transcription	Fetal Stomach	stomach
19	chr5:68514600-68520400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:68514600-68520400	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:68514600-68520400	Weak transcription	Thymus	Thymus
22	chr5:68514600-68522200	Weak transcription	Fetal Thymus	thymus
23	chr5:68514600-68523000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:68514600-68523400	Weak transcription	HSMM	muscle
25	chr5:68514600-68523600	Weak transcription	Ovary	ovary
26	chr5:68514600-68524000	Weak transcription	HSMMtube	muscle
27	chr5:68514800-68516200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:68514800-68521600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:68514800-68521600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:68514800-68521600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:68514800-68523000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:68514800-68523400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:68514800-68523400	Weak transcription	Osteobl	bone
34	chr5:68514800-68523600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:68514800-68524000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr5:68514800-68524000	Weak transcription	NH-A	brain
37	chr5:68514800-68524200	Weak transcription	HUVEC	blood vessel
38	chr5:68514800-68530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:68515000-68516000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:68515000-68517200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:68515000-68517600	Weak transcription	Fetal Intestine Large	intestine
42	chr5:68515000-68523000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:68515000-68523400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:68515000-68524000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:68515000-68524200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:68515000-68530000	Weak transcription	Psoas Muscle	Psoas
47	chr5:68515200-68517800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr5:68515200-68517800	Weak transcription	Primary B cells from cord blood	blood
49	chr5:68515200-68520400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr5:68515200-68520400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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