Variant report

Variant	rs648489
Chromosome Location	chr5:68485366-68485367
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:407)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:407 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr5:68485246-68485945	K562	blood:	n/a	n/a
2	POLR2A	chr5:68484866-68485878	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:68485310-68485843	GM12891	blood:	n/a	n/a
4	POLR2A	chr5:68484537-68486656	SK-N-MC	brain:	n/a	n/a
5	FOS	chr5:68485336-68485797	MCF10A-Er-Src	breast:	n/a	n/a
6	ELF1	chr5:68484925-68485837	K562	blood:	n/a	n/a
7	POLR2A	chr5:68485070-68485855	GM12892	blood:	n/a	n/a
8	REST	chr5:68484909-68485780	K562	blood:	n/a	n/a
9	KAP1	chr5:68484641-68486012	HEK293	kidney:	n/a	n/a
10	CEBPB	chr5:68485038-68485922	MCF-7	breast:	n/a	chr5:68485709-68485720
11	POLR2A	chr5:68484891-68486170	PANC-1	pancreas:	n/a	n/a
12	TAF1	chr5:68484993-68485823	PFSK-1	brain:	n/a	n/a
13	TCF7L2	chr5:68484826-68486084	HEK293	kidney:	n/a	chr5:68485028-68485042
14	POLR2A	chr5:68484538-68485816	MCF10A-Er-Src	breast:	n/a	n/a
15	SIN3A	chr5:68484597-68486202	H1-hESC	embryonic stem cell:	n/a	n/a
16	ELK1	chr5:68485043-68485930	GM12878	blood:	n/a	n/a
17	JUND	chr5:68484894-68485869	H1-hESC	embryonic stem cell:	n/a	n/a
18	TBP	chr5:68485223-68485868	GM12878	blood:	n/a	n/a
19	E2F4	chr5:68485074-68486315	MCF10A-Er-Src	breast:	n/a	chr5:68485393-68485404 chr5:68485396-68485403 chr5:68485870-68485882 chr5:68485396-68485403 chr5:68485396-68485403 chr5:68485392-68485404 chr5:68485395-68485404
20	SP1	chr5:68484947-68485962	A549	lung:	n/a	chr5:68485873-68485882 chr5:68485872-68485886
21	CHD2	chr5:68484773-68486097	K562	blood:	n/a	n/a
22	CHD2	chr5:68485126-68485873	H1-hESC	embryonic stem cell:	n/a	n/a
23	MYC	chr5:68485063-68486410	MCF10A-Er-Src	breast:	n/a	n/a
24	TBL1XR1	chr5:68485164-68486106	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:68485065-68486192	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:68484874-68485924	HUVEC	blood vessel:	n/a	n/a
27	YY1	chr5:68484904-68485568	NT2-D1	testis:	n/a	n/a
28	MAZ	chr5:68484849-68485925	HepG2	liver:	n/a	n/a
29	YY1	chr5:68484693-68485798	ECC-1	luminal epithelium:	n/a	n/a
30	ZKSCAN1	chr5:68485145-68485798	Hela-S3	cervix:	n/a	n/a
31	PML	chr5:68485333-68485759	GM12878	blood:	n/a	n/a
32	RCOR1	chr5:68485097-68485847	GM12878	blood:	n/a	n/a
33	TAL1	chr5:68484836-68486197	K562	blood:	n/a	n/a
34	YY1	chr5:68484866-68485644	HepG2	liver:	n/a	n/a
35	TBL1XR1	chr5:68484578-68486234	K562	blood:	n/a	n/a
36	SP1	chr5:68485285-68485777	H1-hESC	embryonic stem cell:	n/a	n/a
37	BHLHE40	chr5:68485084-68485916	GM12878	blood:	n/a	n/a
38	RUNX3	chr5:68484941-68485944	GM12878	blood:	n/a	chr5:68485304-68485321
39	YY1	chr5:68484814-68485693	GM12892	blood:	n/a	n/a
40	YY1	chr5:68484796-68485646	SK-N-SH_RA	brain:	n/a	n/a
41	ATF3	chr5:68484704-68485741	A549	lung:	n/a	n/a
42	POLR2A	chr5:68484956-68485867	HUVEC	blood vessel:	n/a	n/a
43	SP1	chr5:68485208-68485757	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:68485015-68485805	Gliobla	brain:	n/a	n/a
45	MAX	chr5:68484747-68486335	HCT-116	colon:	n/a	n/a
46	MAX	chr5:68484567-68485886	SK-N-SH	brain:	n/a	n/a
47	SIN3AK20	chr5:68484764-68485814	A549	lung:	n/a	n/a
48	CEBPB	chr5:68485254-68486052	A549	lung:	n/a	chr5:68485709-68485720
49	SIN3AK20	chr5:68484969-68485507	A549	lung:	n/a	n/a
50	POLR2A	chr5:68484869-68486077	U87	brain:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:159131599..159132187-chr5:68485010..68485817,2	HCT-116	colon:
2	chr5:68484208..68487030-chr5:68662372..68666589,5	K562	blood:
3	chr5:68472735..68477267-chr5:68482092..68486946,8	MCF-7	breast:
4	chr5:68389777..68391751-chr5:68483907..68486743,2	MCF-7	breast:
5	chr5:68388464..68391397-chr5:68483791..68487195,4	K562	blood:
6	chr5:68388453..68391488-chr5:68483791..68487092,6	K562	blood:
7	chr19:14628733..14629684-chr5:68484952..68485900,2	Hela-S3	cervix:
8	chr11:71790881..71791531-chr5:68484948..68485919,2	NB4	blood:
9	chr5:68483901..68487830-chr5:68528757..68532922,9	K562	blood:
10	chr5:68485320..68486974-chr5:68663729..68665537,2	MCF-7	breast:
11	chr5:68470678..68474023-chr5:68481300..68486180,5	MCF-7	breast:
12	chr5:68484557..68486514-chr5:68663480..68665519,2	MCF-7	breast:
13	chr5:68485299..68487066-chr5:68626120..68629033,4	MCF-7	breast:
14	chr5:68461460..68464018-chr5:68483608..68486992,6	MCF-7	breast:
15	chr5:68484952..68485893-chr6:18264306..18265074,2	Hela-S3	cervix:
16	chr5:68483355..68487362-chr5:68663859..68666403,7	K562	blood:
17	chr5:68484254..68487485-chr5:68512131..68515372,4	K562	blood:
18	chr5:68483023..68488056-chr5:68511952..68517380,10	K562	blood:

No data

Variant related genes	Relation type
CENPH	TF binding region
ENSG00000134057	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000134058	Chromatin interaction
ENSG00000152942	Chromatin interaction
ENSG00000184154	Chromatin interaction
ENSG00000137497	Chromatin interaction
ENSG00000124795	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000164124	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs100192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742461	0.87[ASN][1000 genomes]
rs11744596	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11745578	0.87[ASN][1000 genomes]
rs12659146	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13175606	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs151589	0.85[ASN][1000 genomes]
rs163442	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs163443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs163444	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs164386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164388	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164389	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164715	0.85[ASN][1000 genomes]
rs1650779	0.81[ASN][1000 genomes]
rs1683831	0.93[ASN][1000 genomes]
rs184747	0.85[ASN][1000 genomes]
rs2002825	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242351	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs239591	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2450230	0.81[ASN][1000 genomes]
rs2450246	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2637128	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2637129	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28506805	0.93[ASN][1000 genomes]
rs28576332	0.87[ASN][1000 genomes]
rs28693971	0.87[ASN][1000 genomes]
rs2913707	0.84[ASN][1000 genomes]
rs2930944	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930945	0.82[ASN][1000 genomes]
rs2930946	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932770	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932771	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932772	0.83[ASN][1000 genomes]
rs2932773	0.83[ASN][1000 genomes]
rs2932775	0.83[ASN][1000 genomes]
rs2932776	0.83[ASN][1000 genomes]
rs2932777	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932778	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2932780	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932783	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972358	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972373	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972374	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972390	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34845020	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350093	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350094	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs350095	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350099	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350105	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs350107	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.85[ASN][1000 genomes]
rs350119	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs350120	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350123	0.83[ASN][1000 genomes]
rs350124	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350125	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs351424	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs352626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353656	0.83[ASN][1000 genomes]
rs375285	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376768	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs379106	0.81[ASN][1000 genomes]
rs379434	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs386640	0.85[ASN][1000 genomes]
rs389686	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs389938	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs390169	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs395122	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs419902	0.85[ASN][1000 genomes]
rs437665	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs444305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs476125	0.93[ASN][1000 genomes]
rs4976159	0.88[ASN][1000 genomes]
rs4976188	0.88[ASN][1000 genomes]
rs651076	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6862253	0.87[ASN][1000 genomes]
rs693725	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7719040	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs648489	MRPS36	cis	multi-tissue	Pritchard
rs648489	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs648489	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68484200-68485800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:68484200-68485800	Active TSS	Brain Germinal Matrix	brain
3	chr5:68484400-68485600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:68484400-68485600	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr5:68484400-68485600	Active TSS	HSMMtube	muscle
6	chr5:68484400-68485600	Active TSS	NH-A	brain
7	chr5:68484400-68485800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:68484400-68485800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr5:68484400-68485800	Active TSS	Fetal Brain Female	brain
10	chr5:68484400-68485800	Bivalent/Poised TSS	HepG2	liver
11	chr5:68484400-68485800	Active TSS	NHLF	lung
12	chr5:68484400-68486000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:68484400-68486000	Active TSS	NHEK	skin
14	chr5:68484400-68486200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:68484400-68486200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:68484400-68486200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr5:68484400-68486200	Active TSS	Fetal Brain Male	brain
18	chr5:68484400-68486200	Active TSS	HSMM	muscle
19	chr5:68484400-68486200	Active TSS	NHDF-Ad	bronchial
20	chr5:68484400-68486400	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:68484400-68486400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr5:68484400-68486400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:68484400-68486400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:68484400-68486400	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr5:68484400-68486400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:68484400-68486400	Active TSS	Fetal Intestine Large	intestine
27	chr5:68484400-68486400	Active TSS	Fetal Intestine Small	intestine
28	chr5:68484400-68486400	Active TSS	Fetal Kidney	kidney
29	chr5:68484400-68486600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:68484400-68486600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr5:68484400-68486600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr5:68484400-68486600	Active TSS	K562	blood
33	chr5:68484400-68487000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr5:68484400-68487000	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr5:68484600-68485400	Active TSS	Pancreas	Pancrea
36	chr5:68484600-68485600	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr5:68484600-68485800	Active TSS	Colonic Mucosa	Colon
38	chr5:68484600-68486000	Active TSS	Gastric	stomach
39	chr5:68484600-68486200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr5:68484600-68486200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:68484600-68486200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:68484600-68486200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr5:68484600-68486200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr5:68484600-68486200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr5:68484600-68486200	Flanking Active TSS	Liver	Liver
46	chr5:68484600-68486200	Active TSS	Fetal Muscle Trunk	muscle
47	chr5:68484600-68486200	Active TSS	Psoas Muscle	Psoas
48	chr5:68484600-68486200	Active TSS	Right Atrium	heart
49	chr5:68484600-68486200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr5:68484600-68486400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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