Variant report

Variant	rs6832168
Chromosome Location	chr4:57332386-57332387
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57331245-57334046	U87	brain:	n/a	n/a
2	WRNIP1	chr4:57332374-57332500	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:57331687-57332520	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:57331562-57334533	K562	blood:	n/a	n/a
5	POLR2A	chr4:57332106-57333166	ProgFib	skin:	n/a	n/a
6	SMC3	chr4:57331762-57332402	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr4:57326457-57334588	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:57331997-57332419	K562	blood:	n/a	n/a
9	POLR2A	chr4:57331789-57334515	K562	blood:	n/a	n/a
10	GATA2	chr4:57331821-57332908	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr4:57329051-57334155	U87	brain:	n/a	n/a
12	POLR2A	chr4:57331455-57334496	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr4:57328023-57334626	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr4:57331299-57334736	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr4:57331991-57334461	K562	blood:	n/a	n/a
16	POLR2A	chr4:57331814-57334536	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr4:57331961-57332460	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr4:57331693-57334461	IMR90	lung:	n/a	n/a
19	POLR2A	chr4:57329197-57334826	HepG2	liver:	n/a	n/a
20	POLR2A	chr4:57331405-57334615	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:57331275-57334493	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr4:57327841-57334590	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr4:57331349-57334520	K562	blood:	n/a	n/a
24	POLR2A	chr4:57331654-57332537	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr4:57331394-57334457	K562	blood:	n/a	n/a
26	MXI1	chr4:57331555-57335556	SK-N-SH	brain:	n/a	chr4:57334126-57334135
27	POLR2A	chr4:57321294-57335320	K562	blood:	n/a	n/a
28	EP300	chr4:57332365-57332822	K562	blood:	n/a	n/a
29	POLR2A	chr4:57331404-57332442	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr4:57331799-57332446	GM12892	blood:	n/a	n/a
31	POLR2A	chr4:57328291-57334478	K562	blood:	n/a	n/a
32	NR2F2	chr4:57332352-57334342	K562	blood:	n/a	chr4:57332711-57332726 chr4:57333758-57333773
33	ZNF384	chr4:57331880-57333884	K562	blood:	n/a	n/a
34	POLR2A	chr4:57328090-57334773	GM12878	blood:	n/a	n/a
35	POLR2A	chr4:57331896-57334479	K562	blood:	n/a	n/a
36	POLR2A	chr4:57326028-57334384	Hela-S3	cervix:	n/a	n/a
37	JUND	chr4:57331867-57334005	K562	blood:	n/a	chr4:57332778-57332789
38	POLR2A	chr4:57331537-57334905	GM12878	blood:	n/a	n/a
39	MTA3	chr4:57331561-57332404	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:57331371-57332647	MCF-7	breast:	n/a	n/a
41	POLR2A	chr4:57331807-57334697	K562	blood:	n/a	n/a
42	POLR2A	chr4:57329895-57334760	MCF10A-Er-Src	breast:	n/a	n/a
43	GABPA	chr4:57332324-57334608	MCF-7	breast:	n/a	n/a
44	GABPA	chr4:57332381-57333049	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr4:57329661-57334500	U87	brain:	n/a	n/a
46	POLR2A	chr4:57332261-57332958	HCT-116	colon:	n/a	n/a
47	POLR2A	chr4:57331436-57332421	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57251940..57255035-chr4:57332077..57334754,4	MCF-7	breast:
2	chr4:57331783..57334990-chr4:57394745..57398997,7	K562	blood:
3	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
4	chr4:57297540..57304787-chr4:57330316..57336934,28	K562	blood:
5	chr4:57332264..57334926-chr4:57844078..57846239,2	MCF-7	breast:
6	chr4:57252171..57255208-chr4:57332200..57335252,5	K562	blood:
7	chr4:57332287..57335313-chr4:57842375..57846822,5	K562	blood:
8	chr4:57300865..57304829-chr4:57331110..57333239,4	MCF-7	breast:
9	chr4:57332142..57335262-chr4:57394352..57398997,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPAT-1	chr4:57327536-57333761	NONHSAT096505

No data

Variant related genes	Relation type
SRP72	TF binding region
ENSG00000128050	Chromatin interaction
ENSG00000157426	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000269921	Chromatin interaction
ENSG00000249693	Chromatin interaction
ENSG00000128059	Chromatin interaction
ENSG00000084092	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10007967	0.87[EUR][1000 genomes]
rs10015634	0.87[EUR][1000 genomes]
rs10518	0.87[EUR][1000 genomes]
rs10866433	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11610	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12646703	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12648503	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1356787	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17086793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086803	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17086883	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17086887	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4073691	0.93[EUR][1000 genomes]
rs4383672	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4524447	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4615235	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4616819	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4865104	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4865105	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4865110	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57523479	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58975286	0.82[AFR][1000 genomes]
rs6584	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66599079	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68101565	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811482	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6811821	0.87[EUR][1000 genomes]
rs6816218	0.87[EUR][1000 genomes]
rs6816268	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6818715	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6820417	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6830518	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6842307	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6843587	0.93[EUR][1000 genomes]
rs6848187	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670198	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7689163	0.84[AFR][1000 genomes]
rs7700034	0.87[EUR][1000 genomes]
rs9312675	0.87[EUR][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6832168	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs6832168	SRP72	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57328800-57332800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:57330200-57332800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr4:57330800-57332800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:57330800-57333000	Enhancers	Spleen	Spleen
5	chr4:57331000-57332600	Enhancers	Stomach Mucosa	stomach
6	chr4:57331400-57332600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:57331400-57332600	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:57331400-57332600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr4:57331400-57332600	Flanking Active TSS	NHEK	skin
10	chr4:57331400-57332800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:57331400-57332800	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:57331400-57334800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr4:57331600-57332400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:57331600-57332400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr4:57331600-57332400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr4:57331600-57332400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:57331600-57332400	Enhancers	Liver	Liver
18	chr4:57331600-57332400	Enhancers	Placenta	Placenta
19	chr4:57331600-57332400	Genic enhancers	Fetal Stomach	stomach
20	chr4:57331600-57332400	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr4:57331600-57332400	Flanking Active TSS	GM12878-XiMat	blood
22	chr4:57331600-57332400	Flanking Active TSS	HSMMtube	muscle
23	chr4:57331600-57332400	Flanking Active TSS	NH-A	brain
24	chr4:57331600-57332600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:57331600-57332600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:57331600-57332600	Enhancers	Primary B cells from cord blood	blood
27	chr4:57331600-57332600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr4:57331600-57332600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr4:57331600-57332600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:57331600-57332600	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr4:57331600-57332600	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr4:57331600-57332600	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr4:57331600-57332600	Enhancers	Fetal Muscle Leg	muscle
34	chr4:57331600-57332600	Enhancers	Fetal Thymus	thymus
35	chr4:57331600-57332600	Flanking Active TSS	Ovary	ovary
36	chr4:57331600-57332600	Flanking Active TSS	Hela-S3	cervix
37	chr4:57331600-57332600	Flanking Active TSS	HSMM	muscle
38	chr4:57331600-57332600	Flanking Active TSS	NHDF-Ad	bronchial
39	chr4:57331600-57332600	Flanking Active TSS	Osteobl	bone
40	chr4:57331600-57332800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr4:57331600-57332800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr4:57331600-57333000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:57331600-57333000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:57331600-57333000	Flanking Active TSS	Fetal Brain Female	brain
45	chr4:57331600-57333000	Flanking Active TSS	Dnd41	blood
46	chr4:57331600-57333600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:57331600-57335000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:57331800-57332400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr4:57331800-57332400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:57331800-57332400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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