Variant report

Variant	rs2932780
Chromosome Location	chr5:68532205-68532206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68483901..68487830-chr5:68528757..68532922,9	K562	blood:
2	chr5:68389043..68391533-chr5:68531972..68533931,2	K562	blood:
3	chr5:68512355..68516868-chr5:68528060..68533660,10	K562	blood:
4	chr5:68529171..68532388-chr5:68663415..68666737,3	K562	blood:
5	chr5:68512355..68517480-chr5:68528060..68532261,10	K562	blood:
6	chr5:68530945..68532461-chr5:68661059..68663307,2	K562	blood:
7	chr5:68512209..68515422-chr5:68529314..68532677,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152942	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs100192	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10940209	0.85[ASN][1000 genomes]
rs10940210	0.84[ASN][1000 genomes]
rs11742461	0.88[ASN][1000 genomes]
rs11744596	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11745578	0.88[ASN][1000 genomes]
rs12652119	0.81[ASN][1000 genomes]
rs12659146	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13175606	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs163442	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs163443	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs163444	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs164386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs164388	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs164389	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs164390	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1683831	0.87[ASN][1000 genomes]
rs2002825	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130757	0.85[ASN][1000 genomes]
rs2171148	0.85[ASN][1000 genomes]
rs2172056	0.85[ASN][1000 genomes]
rs2242351	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291519	0.85[ASN][1000 genomes]
rs2291520	0.85[ASN][1000 genomes]
rs239591	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2450246	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2637128	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2637129	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28506805	0.87[ASN][1000 genomes]
rs28576332	0.88[ASN][1000 genomes]
rs28602964	0.83[ASN][1000 genomes]
rs28693971	0.88[ASN][1000 genomes]
rs2930944	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2930946	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2930949	0.85[ASN][1000 genomes]
rs2930951	0.85[ASN][1000 genomes]
rs2932770	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932771	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932772	0.80[ASN][1000 genomes]
rs2932773	0.80[ASN][1000 genomes]
rs2932775	0.80[ASN][1000 genomes]
rs2932776	0.80[ASN][1000 genomes]
rs2932777	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932778	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932782	0.84[ASN][1000 genomes]
rs2932783	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972358	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972361	0.85[ASN][1000 genomes]
rs2972366	0.85[ASN][1000 genomes]
rs2972373	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972374	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2972381	0.85[ASN][1000 genomes]
rs2972386	0.85[ASN][1000 genomes]
rs2972387	0.85[ASN][1000 genomes]
rs2972388	0.84[ASN][1000 genomes]
rs2972390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34845020	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350093	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs350094	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs350095	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350099	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350105	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs350107	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs350119	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs350120	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350123	0.80[ASN][1000 genomes]
rs350124	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350125	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351424	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs352626	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs375285	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs376768	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs379434	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs389686	0.88[ASW][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs389938	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390169	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3934528	0.84[ASN][1000 genomes]
rs395122	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077460	0.84[ASN][1000 genomes]
rs4362903	0.84[ASN][1000 genomes]
rs437665	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4421064	0.84[ASN][1000 genomes]
rs444305	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4541612	0.82[ASN][1000 genomes]
rs476125	0.87[ASN][1000 genomes]
rs4976159	0.89[ASN][1000 genomes]
rs4976188	0.90[ASN][1000 genomes]
rs62373164	0.84[ASN][1000 genomes]
rs648489	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651076	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6862253	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6876783	0.84[ASN][1000 genomes]
rs693725	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7719040	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs875459	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[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
rs2932780	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs2932780	CDK7	cis	Muscle Skeletal	GTEx
rs2932780	CCDC125	cis	Muscle Skeletal	GTEx
rs2932780	MRPS36	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68529800-68533000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:68530000-68532400	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr5:68530000-68532600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:68530200-68532400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:68530200-68532400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr5:68530200-68532400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr5:68530200-68532400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:68530200-68532400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr5:68530200-68532400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:68530200-68532400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:68530200-68532800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:68531200-68532400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr5:68531200-68532800	Weak transcription	Gastric	stomach
14	chr5:68531200-68533000	Weak transcription	Lung	lung
15	chr5:68531200-68533000	Weak transcription	Pancreas	Pancrea
16	chr5:68531200-68534200	Weak transcription	Esophagus	oesophagus
17	chr5:68531200-68584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:68531400-68532400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr5:68531400-68532400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:68531400-68532400	Enhancers	Spleen	Spleen
21	chr5:68531400-68532400	Flanking Active TSS	Hela-S3	cervix
22	chr5:68531400-68532400	Flanking Active TSS	HUVEC	blood vessel
23	chr5:68531400-68532400	Flanking Active TSS	Osteobl	bone
24	chr5:68531400-68533000	Enhancers	Left Ventricle	heart
25	chr5:68531400-68533200	Weak transcription	Aorta	Aorta
26	chr5:68531400-68537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr5:68531400-68605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:68531600-68532400	Enhancers	Brain Substantia Nigra	brain
29	chr5:68531600-68532400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr5:68531600-68532800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:68531600-68533800	Enhancers	Primary B cells from peripheral blood	blood
32	chr5:68531600-68554600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:68531800-68532400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr5:68531800-68532400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:68531800-68532400	Enhancers	Primary hematopoietic stem cells	blood
36	chr5:68531800-68532400	Enhancers	Adipose Nuclei	Adipose
37	chr5:68531800-68532400	Enhancers	Brain Angular Gyrus	brain
38	chr5:68531800-68532400	Active TSS	Brain Cingulate Gyrus	brain
39	chr5:68531800-68532400	Enhancers	Brain Hippocampus Middle	brain
40	chr5:68531800-68532400	Enhancers	Duodenum Mucosa	Duodenum
41	chr5:68531800-68532400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr5:68531800-68532400	Enhancers	Fetal Lung	lung
43	chr5:68531800-68532400	Enhancers	Fetal Stomach	stomach
44	chr5:68531800-68532400	Enhancers	Ovary	ovary
45	chr5:68531800-68532400	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr5:68531800-68532400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr5:68531800-68532400	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr5:68531800-68532400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr5:68531800-68532400	Enhancers	HSMM	muscle
50	chr5:68531800-68532800	Weak transcription	Fetal Intestine Small	intestine

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