Variant report

Variant	rs59073951
Chromosome Location	chr5:112574478-112574479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:112572466-112576241	SK-N-SH	brain:	n/a	chr5:112572962-112572976
2	MXI1	chr5:112573008-112574714	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:112574450-112574500	MCF10A-Er-Src	breast:	n/a
2	chr5:112574450-112574500	HRPEpiC	eye:	n/a
3	chr5:112574450-112574500	ovcar-3	ovarian:	n/a
4	chr5:112574450-112574500	HRCEpiC	kidney:	n/a
5	chr5:112574450-112574500	H1-hESC	embryonic stem cell:	embryo
6	chr5:112574450-112574500	SK-N-SH	brain:	n/a
7	chr5:112574450-112574500	AG09309	skin:	n/a
8	chr5:112574450-112574500	PrEC	prostate:	n/a
9	chr5:112574450-112574500	MCF-7	breast:	n/a
10	chr5:112574450-112574500	HCM	heart:	n/a
11	chr5:112574450-112574500	GM12878	blood:	n/a
12	chr5:112574450-112574500	Hela-S3	cervix:	n/a
13	chr5:112574450-112574500	GM12891	blood:	n/a
14	chr5:112574450-112574500	Hepatocyte	liver:	n/a
15	chr5:112574450-112574500	HEEpiC	esophagus:	n/a
16	chr5:112574450-112574500	AG10803	skin:	n/a
17	chr5:112574450-112574500	T-47D	breast:	n/a
18	chr5:112574450-112574500	HPAEpiC	pulmonary alveolar:	n/a
19	chr5:112574450-112574500	RPTEC	kidney:	n/a
20	chr5:112574450-112574500	BE2_C	brain:	n/a
21	chr5:112574450-112574500	ECC-1	luminal epithelium:	n/a
22	chr5:112574450-112574500	K562	blood:	n/a
23	chr5:112574450-112574500	SAEC	small airway:	n/a
24	chr5:112574450-112574500	HAEpiC	amniotic membrane:	n/a
25	chr5:112574450-112574500	CMK	blood:	n/a
26	chr5:112574450-112574500	BJ	skin:	n/a
27	chr5:112574450-112574500	NB4	blood:	n/a
28	chr5:112574450-112574500	HMEC	breast:	n/a
29	chr5:112574450-112574500	AG04449	skin:	fetal
30	chr5:112574450-112574500	SK-N-MC	brain:	n/a
31	chr5:112574450-112574500	SK-N-SH_RA	brain:	n/a
32	chr5:112574450-112574500	AG09319	gingival:	n/a
33	chr5:112574450-112574500	HCT-116	colon:	n/a
34	chr5:112574450-112574500	AG04450	lung:	fetal
35	chr5:112574450-112574500	HepG2	liver:	n/a
36	chr5:112574450-112574500	Jurkat	blood:	n/a
37	chr5:112574450-112574500	NHDF-neo	bronchial:	n/a
38	chr5:112574450-112574500	LNCaP	prostate:	n/a
39	chr5:112574450-112574500	HCPEpiC	choroid plexus:	n/a
40	chr5:112574450-112574500	HCF	heart:	n/a
41	chr5:112574450-112574500	HIPEpiC	eye:	n/a
42	chr5:112574450-112574500	NT2-D1	testis:	n/a
43	chr5:112574450-112574500	GM12892	blood:	n/a
44	chr5:112574450-112574500	HEK293	kidney:	embryo
45	chr5:112574450-112574500	PFSK-1	brain:	n/a
46	chr5:112574450-112574500	A549	lung:	n/a
47	chr5:112574450-112574500	U87	brain:	n/a
48	chr5:112574450-112574500	HNPCEpiC	eye:	n/a
49	chr5:112574450-112574500	HUVEC	blood vessel:	n/a
50	chr5:112574450-112574500	ProgFib	skin:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112563565..112565158-chr5:112572143..112575087,2	MCF-7	breast:

No data

Variant related genes	Relation type
MCC	TF binding region
MCC	CpG island

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10519341	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13355627	0.95[ASN][1000 genomes]
rs17135465	0.95[ASN][1000 genomes]
rs17135473	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17135525	0.82[EUR][1000 genomes]
rs17135541	0.87[EUR][1000 genomes]
rs17135586	0.87[EUR][1000 genomes]
rs17135601	0.87[EUR][1000 genomes]
rs17135607	0.87[EUR][1000 genomes]
rs17135615	0.87[EUR][1000 genomes]
rs17376277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1822487	0.82[EUR][1000 genomes]
rs1822494	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2222145	0.87[EUR][1000 genomes]
rs2900070	0.87[EUR][1000 genomes]
rs34893422	0.90[ASN][1000 genomes]
rs41459745	0.87[EUR][1000 genomes]
rs589147	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59935751	0.82[ASN][1000 genomes]
rs6871668	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6876870	0.91[EUR][1000 genomes]
rs882755	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112548400-112581800	Weak transcription	Fetal Kidney	kidney
2	chr5:112557200-112585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:112561600-112575000	Weak transcription	Right Ventricle	heart
4	chr5:112568600-112575000	Weak transcription	Left Ventricle	heart
5	chr5:112568800-112575200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr5:112569000-112575400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:112569000-112577800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:112569600-112575400	Weak transcription	Fetal Brain Female	brain
9	chr5:112570200-112576200	Enhancers	Fetal Heart	heart
10	chr5:112570800-112580600	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:112571000-112581400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:112571400-112574800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:112571800-112579400	Weak transcription	Esophagus	oesophagus
14	chr5:112572000-112581400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:112572200-112576200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:112572400-112574800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:112572400-112575400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr5:112572400-112580800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:112572400-112590400	Weak transcription	Liver	Liver
20	chr5:112572600-112574600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:112572600-112577200	Weak transcription	HMEC	breast
22	chr5:112572600-112585800	Weak transcription	Pancreas	Pancrea
23	chr5:112572800-112575400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr5:112572800-112578200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:112572800-112581800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:112573200-112574600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:112573400-112575400	Enhancers	Colon Smooth Muscle	Colon
28	chr5:112573400-112579400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:112573600-112575000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:112573600-112575000	Enhancers	Adipose Nuclei	Adipose
31	chr5:112573600-112575600	Enhancers	Fetal Stomach	stomach
32	chr5:112573600-112577400	Weak transcription	Psoas Muscle	Psoas
33	chr5:112573800-112577400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:112574000-112575000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr5:112574000-112575200	Weak transcription	Ovary	ovary
36	chr5:112574000-112575400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:112574000-112575600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:112574000-112576400	Weak transcription	Right Atrium	heart
39	chr5:112574000-112576400	Weak transcription	NHEK	skin
40	chr5:112574000-112576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:112574000-112577600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:112574000-112580200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:112574000-112580400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:112574200-112575200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr5:112574200-112578400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:112574200-112581000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links