Variant report

Variant	rs62636520
Chromosome Location	chr12:49690798-49690799
allele	A/G
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	YY1	chr12:49690791-49691064	K562	blood:	n/a	n/a
2	HMGN3	chr12:49690337-49691445	K562	blood:	n/a	n/a
3	CTCF	chr12:49690667-49690872	MCF-7	breast:	n/a	n/a
4	TCF12	chr12:49690177-49691335	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr12:49690660-49690810	HCPEpiC	choroid plexus:	n/a	n/a
6	CTCF	chr12:49690300-49691111	GM12891	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
7	ZEB1	chr12:49690207-49690961	GM12878	blood:	n/a	n/a
8	BCL3	chr12:49690186-49690852	A549	lung:	n/a	chr12:49690479-49690492 chr12:49690377-49690386
9	CTCF	chr12:49690720-49690870	WERI-Rb-1	eye:	n/a	n/a
10	MAX	chr12:49690713-49690899	K562	blood:	n/a	n/a
11	CTCF	chr12:49690325-49690919	MCF-7	breast:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
12	ELF1	chr12:49690725-49690948	K562	blood:	n/a	n/a
13	MAX	chr12:49690104-49691625	MCF-7	breast:	n/a	n/a
14	CTCF	chr12:49690740-49690890	AG10803	skin:	n/a	n/a
15	ZBTB7A	chr12:49690083-49690882	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr12:49690740-49690890	GM12871	blood:	n/a	n/a
17	CTCF	chr12:49690760-49690910	GM12870	blood:	n/a	n/a
18	CTCF	chr12:49690330-49690891	H1-hESC	embryonic stem cell:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
19	MAX	chr12:49690369-49691553	MCF-7	breast:	n/a	n/a
20	CTCF	chr12:49690679-49690857	NHEK	skin:	n/a	n/a
21	KAP1	chr12:49690111-49691292	HEK293	kidney:	n/a	n/a
22	CTCF	chr12:49690292-49690871	T-47D	breast:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
23	MAX	chr12:49690287-49691498	K562	blood:	n/a	n/a
24	E2F6	chr12:49690381-49691384	K562	blood:	n/a	chr12:49690476-49690485
25	CTCF	chr12:49690718-49690842	A549	lung:	n/a	n/a
26	CTCF	chr12:49690321-49690825	GM19240	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
27	CTCF	chr12:49690140-49691627	K562	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
28	CTCF	chr12:49690720-49690855	GM10266	blood:	n/a	n/a
29	CTCF	chr12:49690740-49690890	BE2_C	brain:	n/a	n/a
30	CTCF	chr12:49690266-49690853	GM12878	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
31	CTBP2	chr12:49690112-49691263	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr12:49690699-49690816	GM10248	blood:	n/a	n/a
33	GABPA	chr12:49690428-49691080	K562	blood:	n/a	n/a
34	CTCF	chr12:49690700-49690850	GM12865	blood:	n/a	n/a
35	RCOR1	chr12:49690284-49690897	K562	blood:	n/a	n/a
36	CTCF	chr12:49690659-49690827	GM19239	blood:	n/a	n/a
37	CTCFL	chr12:49690672-49690860	K562	blood:	n/a	n/a
38	UBTF	chr12:49690622-49691119	K562	blood:	n/a	n/a
39	CTCF	chr12:49690143-49691597	HCT-116	colon:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
40	CTCFL	chr12:49690655-49690824	K562	blood:	n/a	n/a
41	TCF12	chr12:49690083-49691415	A549	lung:	n/a	n/a
42	MAX	chr12:49690212-49691624	ECC-1	luminal epithelium:	n/a	n/a
43	CTCF	chr12:49690740-49690890	HMF	breast:	n/a	n/a
44	MAX	chr12:49690213-49691578	ECC-1	luminal epithelium:	n/a	n/a
45	CREB1	chr12:49690747-49691192	A549	lung:	n/a	n/a
46	CTCF	chr12:49690274-49691449	GM12892	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
47	SUZ12	chr12:49688864-49691189	H1-hESC	embryonic stem cell:	n/a	n/a
48	E2F6	chr12:49690753-49691389	A549	lung:	n/a	n/a
49	MAX	chr12:49690261-49691504	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr12:49690726-49690828	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49689988..49692308-chr12:49713640..49717456,5	K562	blood:
2	chr12:49686580..49692358-chr12:49712251..49718367,13	MCF-7	breast:
3	chr12:49686386..49687917-chr12:49689353..49691051,2	MCF-7	breast:
4	chr12:49524142..49526154-chr12:49690463..49692891,2	MCF-7	breast:
5	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
6	chr12:49685493..49694205-chr12:49728829..49734805,16	K562	blood:
7	chr12:49664091..49667882-chr12:49690109..49694759,4	K562	blood:
8	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
9	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
10	chr12:49689191..49691482-chr12:49728607..49731292,2	MCF-7	breast:
11	chr12:49689044..49692243-chr12:49760659..49764012,4	MCF-7	breast:
12	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
13	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
14	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:

Variant related genes	Relation type
PRPH	TF binding region
ENSG00000258232	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000135451	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11168952	0.81[EUR][1000 genomes]
rs11168953	0.81[EUR][1000 genomes]
rs11168954	0.81[EUR][1000 genomes]
rs11168955	0.81[EUR][1000 genomes]
rs11542115	0.90[EUR][1000 genomes]
rs12310093	0.81[EUR][1000 genomes]
rs2303614	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3759170	0.81[EUR][1000 genomes]
rs58403142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59965487	0.81[EUR][1000 genomes]
rs61237420	1.00[ASN][1000 genomes]
rs62636517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309133	0.93[ASN][1000 genomes]
rs73306246	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49686600-49692000	Bivalent Enhancer	Placenta	Placenta
2	chr12:49687600-49691000	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr12:49687600-49691000	Weak transcription	Hela-S3	cervix
4	chr12:49687800-49692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr12:49688200-49691400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
6	chr12:49688600-49691800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr12:49689200-49690800	Enhancers	Pancreas	Pancrea
8	chr12:49689200-49691400	Bivalent Enhancer	Liver	Liver
9	chr12:49689400-49690800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr12:49689600-49692600	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr12:49689800-49691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:49690000-49690800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:49690000-49690800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
14	chr12:49690000-49691000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr12:49690200-49690800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
16	chr12:49690200-49691000	Bivalent Enhancer	Brain Substantia Nigra	brain
17	chr12:49690200-49691000	Bivalent Enhancer	Fetal Lung	lung
18	chr12:49690200-49691200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr12:49690200-49691200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
20	chr12:49690200-49691200	Flanking Active TSS	K562	blood
21	chr12:49690200-49691400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:49690200-49691400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
23	chr12:49690200-49691400	Bivalent Enhancer	Fetal Brain Male	brain
24	chr12:49690200-49691600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
25	chr12:49690200-49692000	Bivalent Enhancer	Fetal Thymus	thymus
26	chr12:49690400-49690800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
27	chr12:49690400-49690800	Bivalent Enhancer	Psoas Muscle	Psoas
28	chr12:49690400-49690800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
29	chr12:49690400-49690800	Enhancers	Right Atrium	heart
30	chr12:49690400-49690800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
31	chr12:49690400-49691000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
32	chr12:49690400-49691000	Bivalent Enhancer	Fetal Heart	heart
33	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
34	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
35	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
36	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
37	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
39	chr12:49690400-49691200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
41	chr12:49690400-49691200	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr12:49690400-49691400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
43	chr12:49690400-49691400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
44	chr12:49690400-49691400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:49690400-49691400	Enhancers	Lung	lung
46	chr12:49690400-49691400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
47	chr12:49690400-49691600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr12:49690400-49691600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr12:49690400-49691600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:49690400-49691600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

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