Variant report

Variant	rs57451017
Chromosome Location	chr12:49689009-49689010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr12:49686994-49689288	U2OS	brain:	n/a	chr12:49687857-49687865
2	CTCF	chr12:49688960-49689110	HRPEpiC	eye:	n/a	n/a
3	MYC	chr12:49688803-49689303	NB4	blood:	n/a	n/a
4	MAX	chr12:49688956-49689691	HepG2	liver:	n/a	n/a
5	SUZ12	chr12:49688864-49691189	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr12:49688896-49689727	H1-hESC	embryonic stem cell:	n/a	chr12:49688934-49688944
7	MAX	chr12:49688910-49689672	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr12:49688815-49689320	NB4	blood:	n/a	n/a
9	E2F6	chr12:49688969-49689699	H1-hESC	embryonic stem cell:	n/a	n/a
10	KAP1	chr12:49686318-49689281	HEK293	kidney:	n/a	chr12:49687857-49687865
11	POLR2A	chr12:49688850-49689049	HCT-116	colon:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49688980-49689030	PrEC	prostate:	n/a
2	chr12:49688980-49689030	AG09309	skin:	n/a
3	chr12:49688980-49689030	CMK	blood:	n/a
4	chr12:49688980-49689030	ECC-1	luminal epithelium:	n/a
5	chr12:49688980-49689030	A549	lung:	n/a
6	chr12:49688980-49689030	HNPCEpiC	eye:	n/a
7	chr12:49688980-49689030	HIPEpiC	eye:	n/a
8	chr12:49688980-49689030	GM12878	blood:	n/a
9	chr12:49688980-49689030	ProgFib	skin:	n/a
10	chr12:49688980-49689030	U87	brain:	n/a
11	chr12:49688980-49689030	GM06990	blood:	n/a
12	chr12:49688980-49689030	HCF	heart:	n/a
13	chr12:49688980-49689030	PFSK-1	brain:	n/a
14	chr12:49688980-49689030	GM12892	blood:	n/a
15	chr12:49688980-49689030	IMR90	lung:	fetal
16	chr12:49688980-49689030	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:49688980-49689030	AG10803	skin:	n/a
18	chr12:49688980-49689030	NT2-D1	testis:	n/a
19	chr12:49688980-49689030	SK-N-SH_RA	brain:	n/a
20	chr12:49688980-49689030	GM19239	blood:	n/a
21	chr12:49688980-49689030	Hela-S3	cervix:	n/a
22	chr12:49688980-49689030	SAEC	small airway:	n/a
23	chr12:49688980-49689030	HUVEC	blood vessel:	n/a
24	chr12:49688980-49689030	K562	blood:	n/a
25	chr12:49688980-49689030	BE2_C	brain:	n/a
26	chr12:49688980-49689030	PANC-1	pancreas:	n/a
27	chr12:49688980-49689030	HAEpiC	amniotic membrane:	n/a
28	chr12:49688980-49689030	AG04450	lung:	fetal
29	chr12:49688980-49689030	AG09319	gingival:	n/a
30	chr12:49688980-49689030	NB4	blood:	n/a
31	chr12:49688980-49689030	HCPEpiC	choroid plexus:	n/a
32	chr12:49688980-49689030	HCM	heart:	n/a
33	chr12:49688980-49689030	H1-hESC	embryonic stem cell:	embryo
34	chr12:49688980-49689030	NHDF-neo	bronchial:	n/a
35	chr12:49688980-49689030	T-47D	breast:	n/a
36	chr12:49688980-49689030	HL-60	blood:	n/a
37	chr12:49688980-49689030	AoSMC	blood vessel:	n/a
38	chr12:49688980-49689030	HMEC	breast:	n/a
39	chr12:49688980-49689030	HRCEpiC	kidney:	n/a
40	chr12:49688980-49689030	HepG2	liver:	n/a
41	chr12:49688980-49689030	HEEpiC	esophagus:	n/a
42	chr12:49688980-49689030	LNCaP	prostate:	n/a
43	chr12:49688980-49689030	GM12891	blood:	n/a
44	chr12:49688980-49689030	Caco-2	colon:	n/a
45	chr12:49688980-49689030	SK-N-MC	brain:	n/a
46	chr12:49688980-49689030	HCT-116	colon:	n/a
47	chr12:49688980-49689030	RPTEC	kidney:	n/a
48	chr12:49688980-49689030	Jurkat	blood:	n/a
49	chr12:49688980-49689030	NHBE	bronchial:	n/a
50	chr12:49688980-49689030	HEK293	kidney:	embryo

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49686580..49692358-chr12:49712251..49718367,13	MCF-7	breast:
2	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
3	chr12:49685493..49694205-chr12:49728829..49734805,16	K562	blood:
4	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
5	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
6	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
7	chr12:49687485..49689033-chr12:49958204..49960498,2	K562	blood:
8	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
9	chr12:49665854..49668915-chr12:49685671..49689413,3	MCF-7	breast:
10	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:

No data

Variant related genes	Relation type
PRPH	TF binding region
PRPH	CpG island
ENSG00000186897	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000258101	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10875946	1.00[ASN][1000 genomes]
rs10875948	1.00[ASN][1000 genomes]
rs11168967	1.00[ASN][1000 genomes]
rs11168970	1.00[ASN][1000 genomes]
rs11168971	1.00[ASN][1000 genomes]
rs11168972	1.00[ASN][1000 genomes]
rs11835037	1.00[ASN][1000 genomes]
rs11837234	1.00[ASN][1000 genomes]
rs12301545	1.00[ASN][1000 genomes]
rs12304800	1.00[ASN][1000 genomes]
rs12313435	1.00[ASN][1000 genomes]
rs12315095	1.00[ASN][1000 genomes]
rs12315130	1.00[ASN][1000 genomes]
rs12317532	1.00[ASN][1000 genomes]
rs12318618	0.93[ASN][1000 genomes]
rs12322335	1.00[ASN][1000 genomes]
rs12322501	0.85[EUR][1000 genomes]
rs12322798	1.00[ASN][1000 genomes]
rs12581307	1.00[AMR][1000 genomes]
rs12581343	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12581428	0.93[ASN][1000 genomes]
rs2070761	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230550	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2236746	1.00[ASN][1000 genomes]
rs28543370	1.00[ASN][1000 genomes]
rs28798494	1.00[ASN][1000 genomes]
rs28823960	1.00[ASN][1000 genomes]
rs28857010	1.00[ASN][1000 genomes]
rs34791911	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898446	1.00[ASN][1000 genomes]
rs4898516	1.00[ASN][1000 genomes]
rs4898517	1.00[ASN][1000 genomes]
rs57755392	1.00[ASN][1000 genomes]
rs60174686	0.82[ASN][1000 genomes]
rs61023481	1.00[ASN][1000 genomes]
rs61455481	1.00[ASN][1000 genomes]
rs7136538	1.00[ASN][1000 genomes]
rs7136945	1.00[ASN][1000 genomes]
rs7294873	1.00[ASN][1000 genomes]
rs7295247	1.00[ASN][1000 genomes]
rs7342318	1.00[ASN][1000 genomes]
rs7342370	1.00[ASN][1000 genomes]
rs7398252	1.00[ASN][1000 genomes]
rs7975431	1.00[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:62 , 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	chr12:49686800-49689400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:49687000-49689200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:49687200-49689200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:49687400-49690000	Bivalent Enhancer	Fetal Thymus	thymus
7	chr12:49687400-49690600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr12:49687600-49689200	Weak transcription	Ovary	ovary
9	chr12:49687600-49690400	Weak transcription	Lung	lung
10	chr12:49687600-49690600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:49687600-49691000	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr12:49687600-49691000	Weak transcription	Hela-S3	cervix
13	chr12:49687800-49690200	Weak transcription	K562	blood
14	chr12:49687800-49692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr12:49688200-49691400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
16	chr12:49688600-49689400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr12:49688600-49689600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:49688600-49691800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr12:49688800-49689200	Bivalent Enhancer	Small Intestine	intestine
20	chr12:49688800-49689600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
21	chr12:49688800-49689600	Bivalent/Poised TSS	HepG2	liver
22	chr12:49688800-49689800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:49688800-49690000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
24	chr12:49688800-49690200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr12:49688800-49690400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr12:49688800-49690400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
27	chr12:49688800-49690400	Weak transcription	A549	lung
28	chr12:49688800-49690600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
29	chr12:49688800-49690600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr12:49689000-49689200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:49689000-49689200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
32	chr12:49689000-49689200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:49689000-49689200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:49689000-49689200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:49689000-49689200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:49689000-49689200	Bivalent Enhancer	Adipose Nuclei	Adipose
37	chr12:49689000-49689200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
38	chr12:49689000-49689200	Bivalent Enhancer	Colonic Mucosa	Colon
39	chr12:49689000-49689200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr12:49689000-49689400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:49689000-49689400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:49689000-49689400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:49689000-49689400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
44	chr12:49689000-49689400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:49689000-49689400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
46	chr12:49689000-49689400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
47	chr12:49689000-49689400	Enhancers	Right Atrium	heart
48	chr12:49689000-49689400	Bivalent Enhancer	Spleen	Spleen
49	chr12:49689000-49689600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr12:49689000-49689600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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