Variant report

Variant	rs2070760
Chromosome Location	chr12:49690337-49690338
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	CTCF	chr12:49690335-49690604	ECC-1	luminal epithelium:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
2	HMGN3	chr12:49690337-49691445	K562	blood:	n/a	n/a
3	TCF12	chr12:49690177-49691335	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr12:49690315-49690643	Medullo	brain:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
5	YY1	chr12:49690323-49690554	HCT-116	colon:	n/a	chr12:49690476-49690485
6	YY1	chr12:49690294-49690686	K562	blood:	n/a	chr12:49690476-49690485
7	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
8	ZEB1	chr12:49690207-49690961	GM12878	blood:	n/a	n/a
9	CTCF	chr12:49690333-49690644	GM10248	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
10	BCL3	chr12:49690186-49690852	A549	lung:	n/a	chr12:49690479-49690492 chr12:49690377-49690386
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	ZNF143	chr12:49690327-49690646	GM12878	blood:	n/a	n/a
13	RUNX3	chr12:49690245-49690646	GM12878	blood:	n/a	n/a
14	MAX	chr12:49690104-49691625	MCF-7	breast:	n/a	n/a
15	CREB1	chr12:49690266-49690698	A549	lung:	n/a	n/a
16	ZBTB7A	chr12:49690083-49690882	ECC-1	luminal epithelium:	n/a	n/a
17	YY1	chr12:49690324-49690593	K562	blood:	n/a	chr12:49690476-49690485
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	CTCF	chr12:49690334-49690635	MCF-7	breast:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
20	KAP1	chr12:49690111-49691292	HEK293	kidney:	n/a	n/a
21	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
22	CEBPB	chr12:49690248-49690554	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr12:49690287-49691498	K562	blood:	n/a	n/a
24	YY1	chr12:49690313-49690547	GM12891	blood:	n/a	chr12:49690476-49690485
25	TCF3	chr12:49690257-49690589	GM12878	blood:	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	chr12:49690273-49690769	MCF-7	breast:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
28	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
29	CTCF	chr12:49690305-49690677	IMR90	lung:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
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	TCF12	chr12:49690209-49690653	A549	lung:	n/a	n/a
32	TCF12	chr12:49690326-49690626	H1-hESC	embryonic stem cell:	n/a	n/a
33	TEAD4	chr12:49690260-49690668	H1-hESC	embryonic stem cell:	n/a	n/a
34	BACH1	chr12:49690331-49690718	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTBP2	chr12:49690112-49691263	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr12:49690336-49690582	K562	blood:	n/a	n/a
37	RCOR1	chr12:49690284-49690897	K562	blood:	n/a	n/a
38	CTCF	chr12:49690328-49690643	GM19239	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
39	RAD21	chr12:49690151-49690725	A549	lung:	n/a	chr12:49690477-49690489 chr12:49690467-49690481 chr12:49690463-49690482 chr12:49690469-49690483
40	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
41	SMC3	chr12:49690332-49690640	GM12878	blood:	n/a	chr12:49690467-49690477 chr12:49690467-49690481
42	TCF12	chr12:49690083-49691415	A549	lung:	n/a	n/a
43	MAX	chr12:49690212-49691624	ECC-1	luminal epithelium:	n/a	n/a
44	TEAD4	chr12:49690250-49690699	K562	blood:	n/a	n/a
45	MAX	chr12:49690213-49691578	ECC-1	luminal epithelium:	n/a	n/a
46	SP1	chr12:49690188-49690720	A549	lung:	n/a	n/a
47	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
48	CTCF	chr12:49690321-49690640	A549	lung:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
49	CTCF	chr12:49690306-49690630	HepG2	liver:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
50	SUZ12	chr12:49688864-49691189	H1-hESC	embryonic stem cell:	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	chr12:49656941..49662685-chr12:49687034..49693573,13	MCF-7	breast:
5	chr12:49685493..49694205-chr12:49728829..49734805,16	K562	blood:
6	chr12:49664091..49667882-chr12:49690109..49694759,4	K562	blood:
7	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
8	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
9	chr12:49689191..49691482-chr12:49728607..49731292,2	MCF-7	breast:
10	chr12:49689044..49692243-chr12:49760659..49764012,4	MCF-7	breast:
11	chr12:49656956..49663896-chr12:49681239..49693031,16	K562	blood:
12	chr12:49657190..49661099-chr12:49688432..49694179,9	K562	blood:
13	chr12:49654800..49660850-chr12:49685742..49692441,19	MCF-7	breast:

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

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10400435	0.85[ASN][1000 genomes]
rs10400567	0.85[ASN][1000 genomes]
rs11168973	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168974	0.92[ASN][1000 genomes]
rs11168975	0.92[ASN][1000 genomes]
rs11503617	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11835037	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11835303	0.89[ASN][1000 genomes]
rs12301545	0.80[AMR][1000 genomes]
rs12313488	0.96[ASN][1000 genomes]
rs12315095	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12315130	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12317532	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12322335	0.80[AMR][1000 genomes]
rs12322783	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12580931	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822293	0.85[ASN][1000 genomes]
rs2236746	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28493849	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28543370	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28691217	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28798494	0.81[EUR][1000 genomes]
rs28857010	0.82[EUR][1000 genomes]
rs3088008	0.89[ASN][1000 genomes]
rs4243545	0.89[ASN][1000 genomes]
rs4898504	0.96[ASN][1000 genomes]
rs4898515	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4898519	0.92[ASN][1000 genomes]
rs57241318	0.92[ASN][1000 genomes]
rs59575791	0.89[ASN][1000 genomes]
rs61023481	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67236923	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67309388	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68030039	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7136538	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7136945	0.80[AMR][1000 genomes]
rs7294873	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7295247	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73112143	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309977	0.89[ASN][1000 genomes]
rs7342318	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7342370	0.80[AMR][1000 genomes]
rs7342384	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7488343	1.00[ASN][1000 genomes]
rs7976060	0.81[AMR][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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49686600-49692000	Bivalent Enhancer	Placenta	Placenta
2	chr12:49687400-49690600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr12:49687600-49690400	Weak transcription	Lung	lung
4	chr12:49687600-49690600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:49687600-49691000	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr12:49687600-49691000	Weak transcription	Hela-S3	cervix
7	chr12:49687800-49692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:49688200-49691400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
9	chr12:49688600-49691800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr12:49688800-49690400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr12:49688800-49690400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
12	chr12:49688800-49690400	Weak transcription	A549	lung
13	chr12:49688800-49690600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
14	chr12:49688800-49690600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr12:49689000-49690400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
16	chr12:49689000-49690400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
17	chr12:49689000-49690600	Bivalent Enhancer	Primary B cells from cord blood	blood
18	chr12:49689000-49690600	Enhancers	Gastric	stomach
19	chr12:49689200-49690400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:49689200-49690600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr12:49689200-49690600	Bivalent Enhancer	Esophagus	oesophagus
22	chr12:49689200-49690600	Bivalent Enhancer	NHEK	skin
23	chr12:49689200-49690800	Enhancers	Pancreas	Pancrea
24	chr12:49689200-49691400	Bivalent Enhancer	Liver	Liver
25	chr12:49689400-49690400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:49689400-49690400	Bivalent Enhancer	Adipose Nuclei	Adipose
27	chr12:49689400-49690400	Weak transcription	Ovary	ovary
28	chr12:49689400-49690400	Weak transcription	Right Atrium	heart
29	chr12:49689400-49690600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
30	chr12:49689400-49690600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:49689400-49690800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr12:49689600-49690600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:49689600-49690600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:49689600-49690600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:49689600-49690600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:49689600-49690600	Enhancers	Right Ventricle	heart
37	chr12:49689600-49692600	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr12:49689800-49690400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:49689800-49690400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr12:49689800-49690600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
41	chr12:49689800-49691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:49690000-49690400	Bivalent Enhancer	Primary T cells from cord blood	blood
43	chr12:49690000-49690400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr12:49690000-49690600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:49690000-49690600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
46	chr12:49690000-49690800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:49690000-49690800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
48	chr12:49690000-49691000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
49	chr12:49690200-49690400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
50	chr12:49690200-49690400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine

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