Variant report

Variant	rs17553240
Chromosome Location	chr5:112258392-112258393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr5:112256585-112258414	MCF-7	breast:	n/a	chr5:112257583-112257593 chr5:112257346-112257356 chr5:112257539-112257549 chr5:112258101-112258110
2	POLR2A	chr5:112256715-112260053	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:112256673-112259684	GM19099	blood:	n/a	n/a
4	MTA3	chr5:112258022-112259737	GM12878	blood:	n/a	n/a
5	RUNX3	chr5:112257459-112258578	GM12878	blood:	n/a	n/a
6	CTCF	chr5:112258300-112258450	HAc	cerebellar:	n/a	n/a
7	EP300	chr5:112257793-112258705	GM12878	blood:	n/a	chr5:112257963-112257979
8	REST	chr5:112256602-112258553	H1-neurons	neurons:	n/a	chr5:112257534-112257544 chr5:112257910-112257930 chr5:112257705-112257725 chr5:112258081-112258090 chr5:112257295-112257308 chr5:112257709-112257722 chr5:112257712-112257725 chr5:112257706-112257724 chr5:112257705-112257725
9	SIN3AK20	chr5:112256389-112258447	MCF-7	breast:	n/a	n/a
10	CTCF	chr5:112256372-112258587	SK-N-SH	brain:	n/a	chr5:112257368-112257381 chr5:112257706-112257719
11	EP300	chr5:112257524-112258485	ECC-1	luminal epithelium:	n/a	chr5:112257963-112257979 chr5:112257527-112257543 chr5:112257539-112257555
12	EGR1	chr5:112257602-112258474	HCT-116	colon:	n/a	chr5:112258096-112258109 chr5:112258099-112258108 chr5:112258097-112258108 chr5:112258187-112258197 chr5:112258184-112258197 chr5:112258096-112258109 chr5:112258096-112258109 chr5:112257605-112257615 chr5:112258055-112258069 chr5:112257756-112257766 chr5:112258096-112258109 chr5:112258099-112258109
13	MAX	chr5:112256560-112258396	A549	lung:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
14	RAD21	chr5:112257767-112258426	A549	lung:	n/a	chr5:112258088-112258102
15	MXI1	chr5:112255540-112258753	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr5:112258320-112258470	AG09319	gingival:	n/a	n/a
17	EGR1	chr5:112257679-112258394	MCF-7	breast:	n/a	chr5:112258096-112258109 chr5:112258099-112258108 chr5:112258097-112258108 chr5:112258187-112258197 chr5:112258184-112258197 chr5:112258096-112258109 chr5:112258096-112258109 chr5:112258055-112258069 chr5:112257756-112257766 chr5:112258096-112258109 chr5:112258099-112258109
18	POLR2A	chr5:112256549-112259966	GM12891	blood:	n/a	n/a
19	TCF12	chr5:112256596-112258395	ECC-1	luminal epithelium:	n/a	chr5:112257259-112257269 chr5:112257548-112257558
20	HCFC1	chr5:112256489-112258699	Hela-S3	cervix:	n/a	n/a
21	MXI1	chr5:112256654-112258725	GM12878	blood:	n/a	n/a
22	ZNF263	chr5:112256253-112258851	HEK293-T-REx	kidney:	n/a	n/a
23	SMC3	chr5:112257013-112258855	SK-N-SH	brain:	n/a	n/a
24	FOXM1	chr5:112257707-112258844	GM12878	blood:	n/a	n/a
25	PML	chr5:112256656-112258400	GM12878	blood:	n/a	n/a
26	SMARCC1	chr5:112256579-112258489	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr5:112256080-112258776	IMR90	lung:	n/a	n/a
28	HDAC2	chr5:112257242-112258428	MCF-7	breast:	n/a	n/a
29	MAZ	chr5:112257710-112258598	GM12878	blood:	n/a	chr5:112258184-112258193 chr5:112257755-112257765
30	MAZ	chr5:112256381-112259049	IMR90	lung:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
31	EBF1	chr5:112257967-112258398	GM12878	blood:	n/a	n/a
32	MAX	chr5:112256888-112258871	GM12878	blood:	n/a	chr5:112257350-112257360 chr5:112258184-112258193 chr5:112257755-112257765
33	RAD21	chr5:112257605-112258556	SK-N-SH	brain:	n/a	chr5:112258088-112258102 chr5:112257705-112257719
34	STAT3	chr5:112258299-112258479	MCF10A-Er-Src	breast:	n/a	n/a
35	CHD1	chr5:112257861-112258438	GM12878	blood:	n/a	n/a
36	CHD2	chr5:112257763-112258417	GM12878	blood:	n/a	n/a
37	RELA	chr5:112256928-112258535	GM15510	blood:	n/a	n/a
38	BCLAF1	chr5:112257656-112258408	GM12878	blood:	n/a	chr5:112257949-112257958
39	CTCF	chr5:112258360-112258510	GM12874	blood:	n/a	n/a
40	POLR2A	chr5:112256847-112258484	GM12892	blood:	n/a	n/a
41	ZBTB7A	chr5:112256674-112258405	ECC-1	luminal epithelium:	n/a	n/a
42	TBL1XR1	chr5:112257926-112258477	K562	blood:	n/a	n/a
43	CTCF	chr5:112256618-112258726	A549	lung:	n/a	chr5:112257368-112257381 chr5:112257706-112257719
44	MTA3	chr5:112256485-112259930	GM12878	blood:	n/a	n/a
45	SMC3	chr5:112257815-112258581	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:112258374-112258424	AG10803	skin:	n/a
2	chr5:112258374-112258424	SAEC	small airway:	n/a
3	chr5:112258374-112258424	CMK	blood:	n/a
4	chr5:112258374-112258424	AoSMC	blood vessel:	n/a
5	chr5:112258374-112258424	HMEC	breast:	n/a
6	chr5:112258374-112258424	GM06990	blood:	n/a
7	chr5:112258374-112258424	HepG2	liver:	n/a
8	chr5:112258374-112258424	T-47D	breast:	n/a
9	chr5:112258374-112258424	HAEpiC	amniotic membrane:	n/a
10	chr5:112258374-112258424	GM12892	blood:	n/a
11	chr5:112258374-112258424	HEK293	kidney:	embryo
12	chr5:112258374-112258424	AG04450	lung:	fetal
13	chr5:112258374-112258424	HCM	heart:	n/a
14	chr5:112258374-112258424	ovcar-3	ovarian:	n/a
15	chr5:112258374-112258424	MCF10A-Er-Src	breast:	n/a
16	chr5:112258374-112258424	Hepatocyte	liver:	n/a
17	chr5:112258374-112258424	NB4	blood:	n/a
18	chr5:112258374-112258424	Caco-2	colon:	n/a
19	chr5:112258374-112258424	GM19239	blood:	n/a
20	chr5:112258374-112258424	HRPEpiC	eye:	n/a
21	chr5:112258374-112258424	ECC-1	luminal epithelium:	n/a
22	chr5:112258374-112258424	AG04449	skin:	fetal
23	chr5:112258374-112258424	NH-A	brain:	n/a
24	chr5:112258374-112258424	HPAEpiC	pulmonary alveolar:	n/a
25	chr5:112258374-112258424	MCF-7	breast:	n/a
26	chr5:112258374-112258424	HCF	heart:	n/a
27	chr5:112258374-112258424	IMR90	lung:	fetal
28	chr5:112258374-112258424	NHDF-neo	bronchial:	n/a
29	chr5:112258374-112258424	Jurkat	blood:	n/a
30	chr5:112258374-112258424	GM12878	blood:	n/a
31	chr5:112258374-112258424	HL-60	blood:	n/a
32	chr5:112258374-112258424	A549	lung:	n/a
33	chr5:112258374-112258424	HEEpiC	esophagus:	n/a
34	chr5:112258374-112258424	HCT-116	colon:	n/a
35	chr5:112258374-112258424	AG09309	skin:	n/a
36	chr5:112258374-112258424	HNPCEpiC	eye:	n/a
37	chr5:112258374-112258424	AG09319	gingival:	n/a
38	chr5:112258374-112258424	HRCEpiC	kidney:	n/a
39	chr5:112258374-112258424	PrEC	prostate:	n/a
40	chr5:112258374-112258424	Hela-S3	cervix:	n/a
41	chr5:112258374-112258424	HCPEpiC	choroid plexus:	n/a
42	chr5:112258374-112258424	ProgFib	skin:	n/a
43	chr5:112258374-112258424	SK-N-MC	brain:	n/a
44	chr5:112258374-112258424	HRE	kidney:	n/a
45	chr5:112258374-112258424	SKMC	muscle:	n/a
46	chr5:112258374-112258424	HIPEpiC	eye:	n/a
47	chr5:112258374-112258424	LNCaP	prostate:	n/a
48	chr5:112258374-112258424	BJ	skin:	n/a
49	chr5:112258374-112258424	H1-hESC	embryonic stem cell:	embryo
50	chr5:112258374-112258424	SK-N-SH_RA	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112255914..112262078-chr5:112308752..112315375,16	MCF-7	breast:
2	chr5:112253961..112259306-chr5:112310933..112315767,8	K562	blood:
3	chr5:112196028..112199860-chr5:112256680..112260462,5	MCF-7	breast:
4	chr5:112223765..112227904-chr5:112256681..112259724,3	K562	blood:
5	chr5:112195239..112200315-chr5:112255126..112261929,8	MCF-7	breast:
6	chr5:111496112..111498947-chr5:112256676..112259616,2	K562	blood:
7	chr5:112255209..112259355-chr5:112310614..112316433,9	K562	blood:

Variant related genes	Relation type
REEP5	TF binding region
REEP5	CpG island
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction
ENSG00000172795	Chromatin interaction
ENSG00000212643	Chromatin interaction
ENSG00000238363	Chromatin interaction
ENSG00000224032	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10064080	0.96[EUR][1000 genomes]
rs10447234	1.00[ASN][1000 genomes]
rs10515450	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10515451	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10515452	0.82[EUR][1000 genomes]
rs12152818	1.00[ASN][1000 genomes]
rs12152991	1.00[ASN][1000 genomes]
rs12187307	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12188113	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13354064	0.93[EUR][1000 genomes]
rs13360667	0.96[EUR][1000 genomes]
rs17135215	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28635838	0.89[EUR][1000 genomes]
rs28789211	0.96[EUR][1000 genomes]
rs3962814	0.93[EUR][1000 genomes]
rs4145650	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55915006	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56209573	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56315627	1.00[ASN][1000 genomes]
rs56364425	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56398453	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728347	0.96[EUR][1000 genomes]
rs73227370	0.96[EUR][1000 genomes]
rs73789249	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73789251	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73789252	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73789253	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73789254	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73789266	0.86[AMR][1000 genomes];0.97[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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv2763866	chr5:112254282-112284223	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3393782	chr5:112256103-112258601	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112255400-112258400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:112256200-112258400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr5:112256200-112258600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:112256400-112258400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr5:112256400-112258400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112256400-112258400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr5:112256400-112258400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:112256400-112258400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:112256400-112258400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr5:112256400-112258400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:112256400-112258400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:112256400-112258400	Active TSS	Aorta	Aorta
13	chr5:112256400-112258400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr5:112256400-112258400	Active TSS	Left Ventricle	heart
15	chr5:112256400-112258400	Active TSS	Ovary	ovary
16	chr5:112256400-112258400	Active TSS	Pancreas	Pancrea
17	chr5:112256400-112258400	Active TSS	Right Ventricle	heart
18	chr5:112256400-112258600	Active TSS	Fetal Muscle Trunk	muscle
19	chr5:112256600-112258400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:112256600-112258400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:112256600-112258400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr5:112256600-112258400	Active TSS	Esophagus	oesophagus
23	chr5:112256600-112258400	Active TSS	Fetal Heart	heart
24	chr5:112256600-112258400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr5:112256600-112258600	Active TSS	Fetal Kidney	kidney
26	chr5:112256800-112258400	Active TSS	Fetal Brain Male	brain
27	chr5:112256800-112258400	Active TSS	Osteobl	bone
28	chr5:112257000-112258400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:112257200-112258400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:112257800-112258400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:112257800-112258400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:112257800-112258600	Active TSS	Brain Germinal Matrix	brain
33	chr5:112258000-112258400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
34	chr5:112258000-112258400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:112258000-112258400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr5:112258000-112258400	Flanking Active TSS	NHLF	lung
37	chr5:112258000-112258600	Flanking Active TSS	Colonic Mucosa	Colon
38	chr5:112258000-112258600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr5:112258000-112258600	Flanking Active TSS	Thymus	Thymus
40	chr5:112258000-112259400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:112258000-112259600	Flanking Active TSS	Dnd41	blood
42	chr5:112258000-112259800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr5:112258000-112265000	Weak transcription	Small Intestine	intestine
44	chr5:112258200-112258400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
45	chr5:112258200-112258400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr5:112258200-112258400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:112258200-112258400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr5:112258200-112258400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
49	chr5:112258200-112258400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
50	chr5:112258200-112258400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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