Variant report

Variant	rs7488343
Chromosome Location	chr12:49689597-49689598
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:49689036-49689740	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr12:49689520-49689670	RPTEC	kidney:	n/a	n/a
3	MAX	chr12:49688956-49689691	HepG2	liver:	n/a	n/a
4	SUZ12	chr12:49688864-49691189	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr12:49688896-49689727	H1-hESC	embryonic stem cell:	n/a	chr12:49688934-49688944
6	MAX	chr12:49688910-49689672	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr12:49688969-49689699	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49686580..49692358-chr12:49712251..49718367,13	MCF-7	breast:
2	chr12:49686386..49687917-chr12:49689353..49691051,2	MCF-7	breast:
3	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
4	chr12:49685493..49694205-chr12:49728829..49734805,16	K562	blood:
5	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
6	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
7	chr12:49689191..49691482-chr12:49728607..49731292,2	MCF-7	breast:
8	chr12:49689044..49692243-chr12:49760659..49764012,4	MCF-7	breast:
9	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
10	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
11	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:

No data

Variant related genes	Relation type
PRPH	TF binding region
ENSG00000167553	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000186897	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10400435	0.85[ASN][1000 genomes]
rs10400567	0.85[ASN][1000 genomes]
rs11168973	0.96[ASN][1000 genomes]
rs11168974	0.92[ASN][1000 genomes]
rs11168975	0.92[ASN][1000 genomes]
rs11503617	0.96[ASN][1000 genomes]
rs11835303	0.89[ASN][1000 genomes]
rs12313488	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12580931	1.00[ASN][1000 genomes]
rs12822293	0.85[ASN][1000 genomes]
rs2070760	1.00[ASN][1000 genomes]
rs28493849	1.00[ASN][1000 genomes]
rs3088008	0.89[ASN][1000 genomes]
rs4243545	0.89[ASN][1000 genomes]
rs4898504	0.96[ASN][1000 genomes]
rs4898517	0.82[AMR][1000 genomes]
rs4898519	0.92[ASN][1000 genomes]
rs57241318	0.92[ASN][1000 genomes]
rs59575791	0.89[ASN][1000 genomes]
rs67236923	1.00[ASN][1000 genomes]
rs67309388	1.00[ASN][1000 genomes]
rs73112143	1.00[ASN][1000 genomes]
rs73309977	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	esv19135	chr12:49676002-49690399	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv558834	chr12:49676010-49691567	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
8	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv826367	chr12:49686493-49691709	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49686600-49689800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
2	chr12:49686600-49692000	Bivalent Enhancer	Placenta	Placenta
3	chr12:49687400-49690000	Bivalent Enhancer	Fetal Thymus	thymus
4	chr12:49687400-49690600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr12:49687600-49690400	Weak transcription	Lung	lung
6	chr12:49687600-49690600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:49687600-49691000	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr12:49687600-49691000	Weak transcription	Hela-S3	cervix
9	chr12:49687800-49690200	Weak transcription	K562	blood
10	chr12:49687800-49692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:49688200-49691400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
12	chr12:49688600-49689600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:49688600-49691800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr12:49688800-49689600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr12:49688800-49689600	Bivalent/Poised TSS	HepG2	liver
16	chr12:49688800-49689800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:49688800-49690000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
18	chr12:49688800-49690200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
19	chr12:49688800-49690400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr12:49688800-49690400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr12:49688800-49690400	Weak transcription	A549	lung
22	chr12:49688800-49690600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
23	chr12:49688800-49690600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr12:49689000-49689600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:49689000-49689600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
26	chr12:49689000-49689600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr12:49689000-49689600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:49689000-49689600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:49689000-49689600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
30	chr12:49689000-49689600	Flanking Active TSS	Right Ventricle	heart
31	chr12:49689000-49689600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
32	chr12:49689000-49689600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
33	chr12:49689000-49689800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr12:49689000-49690400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
35	chr12:49689000-49690400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr12:49689000-49690600	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr12:49689000-49690600	Enhancers	Gastric	stomach
38	chr12:49689200-49689600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:49689200-49689600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
40	chr12:49689200-49689600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
41	chr12:49689200-49689800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:49689200-49689800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:49689200-49690400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:49689200-49690600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:49689200-49690600	Bivalent Enhancer	Esophagus	oesophagus
46	chr12:49689200-49690600	Bivalent Enhancer	NHEK	skin
47	chr12:49689200-49690800	Enhancers	Pancreas	Pancrea
48	chr12:49689200-49691400	Bivalent Enhancer	Liver	Liver
49	chr12:49689400-49689600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr12:49689400-49689600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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