Variant report

Variant	rs3745157
Chromosome Location	chr19:45594595-45594596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:181)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:181 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr19:45594158-45594814	SK-N-SH	brain:	n/a	n/a
2	ATF2	chr19:45594226-45595423	H1-hESC	embryonic stem cell:	n/a	n/a
3	SRF	chr19:45594391-45595170	ECC-1	luminal epithelium:	n/a	chr19:45594920-45594933 chr19:45594915-45594932 chr19:45594921-45594932
4	USF1	chr19:45594178-45594605	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:45594337-45595167	GM12878	blood:	n/a	n/a
6	USF1	chr19:45594198-45594814	A549	lung:	n/a	n/a
7	HA-E2F1	chr19:45594385-45595156	MCF-7	breast:	n/a	chr19:45594938-45594947
8	POLR2A	chr19:45593947-45597083	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF7L2	chr19:45594483-45595312	PANC-1	pancreas:	n/a	n/a
10	ATF2	chr19:45594467-45595320	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF7	chr19:45594342-45595208	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr19:45594378-45595176	K562	blood:	n/a	chr19:45594883-45594892
13	GTF2F1	chr19:45594275-45595201	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOSL2	chr19:45594414-45595534	A549	lung:	n/a	n/a
15	GTF2F1	chr19:45594583-45595300	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr19:45594233-45594678	A549	lung:	n/a	n/a
17	ETS1	chr19:45594462-45595385	A549	lung:	n/a	chr19:45594956-45594973
18	POLR2A	chr19:45594165-45596786	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:45594218-45595420	H1-hESC	embryonic stem cell:	n/a	n/a
20	EP300	chr19:45594089-45595503	A549	lung:	n/a	n/a
21	MAX	chr19:45594244-45595415	H1-hESC	embryonic stem cell:	n/a	chr19:45594883-45594892
22	POLR2A	chr19:45594279-45595459	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:45594023-45595665	U87	brain:	n/a	n/a
24	POLR2A	chr19:45594507-45595375	HUVEC	blood vessel:	n/a	n/a
25	EP300	chr19:45594153-45595471	ECC-1	luminal epithelium:	n/a	n/a
26	SP4	chr19:45594379-45595298	H1-hESC	embryonic stem cell:	n/a	chr19:45594936-45594947 chr19:45594906-45594917 chr19:45594934-45594950
27	POLR2A	chr19:45594120-45595147	ECC-1	luminal epithelium:	n/a	n/a
28	MAX	chr19:45594244-45595290	H1-hESC	embryonic stem cell:	n/a	chr19:45594883-45594892
29	POLR2A	chr19:45594332-45595549	GM12891	blood:	n/a	n/a
30	MYC	chr19:45594304-45595240	K562	blood:	n/a	chr19:45594883-45594892
31	MAX	chr19:45594195-45595302	MCF-7	breast:	n/a	chr19:45594883-45594892
32	ELF1	chr19:45594590-45595299	GM12878	blood:	n/a	chr19:45594847-45594859
33	SIN3AK20	chr19:45594327-45595432	A549	lung:	n/a	n/a
34	POLR2A	chr19:45594229-45595408	K562	blood:	n/a	n/a
35	EP300	chr19:45594427-45595468	SK-N-SH	brain:	n/a	n/a
36	USF1	chr19:45594207-45595426	A549	lung:	n/a	n/a
37	PBX3	chr19:45594552-45595368	SK-N-SH	brain:	n/a	n/a
38	MAX	chr19:45594069-45595565	A549	lung:	n/a	chr19:45594883-45594892
39	POLR2A	chr19:45594215-45595189	MCF-7	breast:	n/a	n/a
40	USF1	chr19:45594267-45594863	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr19:45594319-45595279	HEK293	kidney:	n/a	n/a
42	SIX5	chr19:45594325-45595589	A549	lung:	n/a	n/a
43	POLR2A	chr19:45594297-45597124	GM12892	blood:	n/a	n/a
44	YY1	chr19:45594454-45595447	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr19:45594524-45595494	GM12891	blood:	n/a	n/a
46	YY1	chr19:45594577-45595409	H1-hESC	embryonic stem cell:	n/a	n/a
47	GATA3	chr19:45594025-45595554	A549	lung:	n/a	n/a
48	YY1	chr19:45594477-45595126	GM12891	blood:	n/a	n/a
49	POLR2A	chr19:45594118-45595513	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr19:45594213-45595184	A549	lung:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45571923..45576077-chr19:45594481..45600071,10	MCF-7	breast:
2	chr19:45542175..45544773-chr19:45593754..45596386,2	MCF-7	breast:
3	chr19:45394111..45396115-chr19:45593226..45596136,2	MCF-7	breast:
4	chr19:45250268..45252334-chr19:45593239..45597540,3	MCF-7	breast:
5	chr19:45577259..45585589-chr19:45592358..45603656,27	K562	blood:
6	chr19:45576493..45586900-chr19:45588536..45604492,49	MCF-7	breast:
7	chr19:45576986..45585099-chr19:45592126..45598719,16	MCF-7	breast:
8	chr19:45580763..45587822-chr19:45593153..45598212,14	K562	blood:
9	chr19:45503629..45506931-chr19:45593767..45597738,4	K562	blood:
10	chr19:45594586..45596499-chr19:45682181..45685187,4	MCF-7	breast:
11	chr19:45570935..45574142-chr19:45593620..45597765,5	MCF-7	breast:
12	chr19:45503630..45506563-chr19:45593514..45596516,3	MCF-7	breast:
13	chr19:45593518..45596472-chr19:45847951..45849641,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267348	TF binding region
PPP1R37	TF binding region
ENSG00000104856	Chromatin interaction
ENSG00000104892	Chromatin interaction
ENSG00000104859	Chromatin interaction
ENSG00000130204	Chromatin interaction
ENSG00000170684	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000267282	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000069399	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10405859	0.89[LWK][hapmap];0.80[AFR][1000 genomes]
rs11666681	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11672002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12975438	0.80[EUR][1000 genomes]
rs12975698	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs12977416	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12981729	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12984180	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3178166	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35620552	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35836101	0.83[EUR][1000 genomes]
rs7251736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7255018	0.85[EUR][1000 genomes]
rs8108762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8109620	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs968445	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3449420	chr19:45523560-45626884	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv10933	chr19:45588911-45595377	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv828563	chr19:45594591-45598168	Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3745157	GRLF1	cis	parietal	SCAN
rs3745157	MYBPC2	cis	parietal	SCAN
rs3745157	VN1R4	cis	parietal	SCAN
rs3745157	CPT1C	cis	parietal	SCAN
rs3745157	TBC1D17	cis	parietal	SCAN
rs3745157	BIRC8	cis	parietal	SCAN
rs3745157	LIN7B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45583600-45594600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:45583600-45595200	Weak transcription	Small Intestine	intestine
3	chr19:45585800-45594600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:45587800-45594800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:45590600-45594800	Strong transcription	Dnd41	blood
6	chr19:45592200-45594600	Weak transcription	Primary T cells from cord blood	blood
7	chr19:45593200-45595000	ZNF genes & repeats	GM12878-XiMat	blood
8	chr19:45593200-45595400	Strong transcription	HepG2	liver
9	chr19:45593400-45594600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:45593400-45594600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:45593400-45594600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
12	chr19:45593600-45594600	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr19:45593800-45594600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:45593800-45594600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr19:45593800-45594600	Enhancers	Lung	lung
16	chr19:45593800-45594800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:45594000-45594600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:45594000-45594600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr19:45594000-45594600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:45594000-45594600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:45594000-45594600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:45594000-45594600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr19:45594000-45594800	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr19:45594000-45594800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr19:45594000-45594800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr19:45594000-45594800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr19:45594000-45595000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:45594000-45598200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr19:45594200-45594600	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
30	chr19:45594200-45594600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:45594200-45594600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:45594200-45594600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr19:45594200-45594600	Enhancers	Primary B cells from cord blood	blood
34	chr19:45594200-45594600	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr19:45594200-45594600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:45594200-45594600	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr19:45594200-45594600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr19:45594200-45594600	Flanking Active TSS	Esophagus	oesophagus
39	chr19:45594200-45594600	Flanking Active TSS	Fetal Brain Female	brain
40	chr19:45594200-45594600	Flanking Active TSS	Fetal Heart	heart
41	chr19:45594200-45594600	Flanking Active TSS	Fetal Lung	lung
42	chr19:45594200-45594600	Flanking Active TSS	Pancreas	Pancrea
43	chr19:45594200-45594600	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr19:45594200-45594600	Flanking Active TSS	HMEC	breast
45	chr19:45594200-45594600	Flanking Active TSS	NHDF-Ad	bronchial
46	chr19:45594200-45594600	Transcr. at gene 5' and 3'	NHEK	skin
47	chr19:45594200-45594800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr19:45594200-45594800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:45594200-45594800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:45594200-45594800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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