Variant report

Variant	rs4073691
Chromosome Location	chr4:57331107-57331108
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57330681-57331121	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:57330066-57331239	U87	brain:	n/a	n/a
3	POLR2A	chr4:57331088-57331114	K562	blood:	n/a	n/a
4	POLR2A	chr4:57326457-57334588	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:57329051-57334155	U87	brain:	n/a	n/a
6	POLR2A	chr4:57328023-57334626	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr4:57330814-57331143	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:57329789-57332333	U87	brain:	n/a	n/a
9	POLR2A	chr4:57330708-57331125	H1-hESC	embryonic stem cell:	n/a	n/a
10	BCL3	chr4:57330607-57331187	A549	lung:	n/a	n/a
11	POLR2A	chr4:57328174-57331217	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:57329197-57334826	HepG2	liver:	n/a	n/a
13	POLR2A	chr4:57329828-57331377	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:57327841-57334590	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr4:57329439-57331320	MCF-7	breast:	n/a	n/a
16	POLR2A	chr4:57330658-57331195	GM12891	blood:	n/a	n/a
17	MTA3	chr4:57330614-57331154	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:57328083-57331197	A549	lung:	n/a	n/a
19	POLR2A	chr4:57330524-57331347	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr4:57321294-57335320	K562	blood:	n/a	n/a
21	POLR2A	chr4:57327796-57331218	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr4:57328291-57334478	K562	blood:	n/a	n/a
23	POLR2A	chr4:57328090-57334773	GM12878	blood:	n/a	n/a
24	E2F4	chr4:57330941-57331124	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:57330680-57331121	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr4:57326028-57334384	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr4:57329895-57334760	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr4:57329138-57331157	K562	blood:	n/a	n/a
29	POLR2A	chr4:57330605-57331230	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr4:57329172-57332331	GM12891	blood:	n/a	n/a
31	POLR2A	chr4:57329661-57334500	U87	brain:	n/a	n/a
32	POLR2A	chr4:57330575-57331117	GM12892	blood:	n/a	n/a
33	POLR2A	chr4:57330655-57331111	GM12891	blood:	n/a	n/a
34	POLR2A	chr4:57330578-57331174	PANC-1	pancreas:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57298117..57310780-chr4:57324651..57337770,39	MCF-7	breast:
2	chr4:57297540..57304787-chr4:57330316..57336934,28	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
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10007967	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10009543	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10015221	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10015634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10866433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610	0.91[EUR][1000 genomes]
rs11733474	0.94[JPT][hapmap]
rs12648503	0.86[EUR][1000 genomes]
rs13114104	0.93[JPT][hapmap]
rs13147824	0.94[JPT][hapmap]
rs1401912	0.94[JPT][hapmap]
rs17051687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs17086793	0.93[EUR][1000 genomes]
rs17086803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086883	0.86[EUR][1000 genomes]
rs17086887	0.86[EUR][1000 genomes]
rs2049087	0.94[JPT][hapmap]
rs2139512	0.88[JPT][hapmap]
rs28472763	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2899063	0.94[JPT][hapmap]
rs3796547	0.94[JPT][hapmap]
rs3822003	0.94[JPT][hapmap]
rs4167	0.94[JPT][hapmap]
rs4305581	1.00[JPT][hapmap]
rs4615235	0.91[EUR][1000 genomes]
rs4865102	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4865104	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865105	0.83[EUR][1000 genomes]
rs4865110	0.86[EUR][1000 genomes]
rs57523479	0.86[EUR][1000 genomes]
rs58975286	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6554355	0.94[JPT][hapmap]
rs6554356	0.94[JPT][hapmap]
rs66599079	0.86[EUR][1000 genomes]
rs68101565	0.86[EUR][1000 genomes]
rs6811482	0.86[EUR][1000 genomes]
rs6811821	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816218	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819534	0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6820417	0.82[EUR][1000 genomes]
rs6826795	0.94[JPT][hapmap]
rs6832168	0.93[EUR][1000 genomes]
rs6843587	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848187	0.92[EUR][1000 genomes]
rs7670198	0.86[EUR][1000 genomes]
rs7683781	0.94[JPT][hapmap]
rs7692073	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7694047	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7700034	0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312675	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9683679	0.94[JPT][hapmap]
rs9684298	0.94[JPT][hapmap]
rs9996593	0.87[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4073691	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
2	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
3	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:57315000-57331800	Weak transcription	Aorta	Aorta
7	chr4:57318800-57331600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:57319200-57331600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:57322600-57331400	Weak transcription	Fetal Kidney	kidney
10	chr4:57326400-57331800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:57326400-57332000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:57326600-57332200	Weak transcription	Colonic Mucosa	Colon
13	chr4:57326800-57331800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:57327000-57331800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:57327200-57331800	Weak transcription	Gastric	stomach
16	chr4:57327400-57331600	Weak transcription	Lung	lung
17	chr4:57327400-57331800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:57327400-57332200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:57327600-57331800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:57328800-57331200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:57328800-57331200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:57328800-57331400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:57328800-57331600	Weak transcription	Liver	Liver
24	chr4:57328800-57331600	Weak transcription	NH-A	brain
25	chr4:57328800-57331800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr4:57328800-57332000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:57328800-57332200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:57328800-57332800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:57329000-57331400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:57329000-57331400	Weak transcription	Fetal Lung	lung
31	chr4:57329000-57331400	Weak transcription	HUVEC	blood vessel
32	chr4:57329000-57331400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:57329000-57331600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:57329000-57331800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:57329000-57331800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:57329000-57331800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:57329200-57331600	Weak transcription	Primary B cells from cord blood	blood
38	chr4:57329200-57331600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:57329400-57331200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:57329400-57331400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:57329400-57331400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr4:57329400-57331600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:57329400-57331600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:57329400-57331600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:57329400-57331600	Weak transcription	HSMMtube	muscle
46	chr4:57329400-57331800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:57329400-57331800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:57329600-57331400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:57329600-57331600	Weak transcription	Placenta	Placenta
50	chr4:57329600-57331600	Weak transcription	Thymus	Thymus

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