Variant report

Variant	rs2070761
Chromosome Location	chr12:49690509-49690510
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	CTCF	chr12:49690420-49690570	BJ	skin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
3	HMGN3	chr12:49690337-49691445	K562	blood:	n/a	n/a
4	CTCF	chr12:49690356-49690600	MCF-7	breast:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
5	CTCF	chr12:49690380-49690530	HCPEpiC	choroid plexus:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
6	CTCF	chr12:49690364-49690622	HepG2	liver:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
7	TCF12	chr12:49690177-49691335	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr12:49690380-49690530	WI-38	lung:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
9	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
10	SMC3	chr12:49690345-49690603	K562	blood:	n/a	chr12:49690467-49690477 chr12:49690467-49690481
11	CTCF	chr12:49690360-49690510	BJ	skin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
12	CTCF	chr12:49690400-49690550	NHEK	skin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
13	YY1	chr12:49690323-49690554	HCT-116	colon:	n/a	chr12:49690476-49690485
14	YY1	chr12:49690294-49690686	K562	blood:	n/a	chr12:49690476-49690485
15	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
16	ZEB1	chr12:49690207-49690961	GM12878	blood:	n/a	n/a
17	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
18	CTCF	chr12:49690370-49690614	Spleen_OC	spleen:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
19	CTCF	chr12:49690400-49690550	HFF	foreskin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
20	ELF1	chr12:49690367-49690552	K562	blood:	n/a	n/a
21	BCL3	chr12:49690186-49690852	A549	lung:	n/a	chr12:49690479-49690492 chr12:49690377-49690386
22	EBF1	chr12:49690382-49690644	GM12878	blood:	n/a	n/a
23	CBX3	chr12:49690377-49690710	K562	blood:	n/a	n/a
24	CTCF	chr12:49690380-49690530	GM12865	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
25	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
26	CTCF	chr12:49690400-49690550	HCPEpiC	choroid plexus:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
27	ZNF143	chr12:49690327-49690646	GM12878	blood:	n/a	n/a
28	PAX5	chr12:49690412-49690652	GM12878	blood:	n/a	n/a
29	RUNX3	chr12:49690245-49690646	GM12878	blood:	n/a	n/a
30	CTCF	chr12:49690400-49690550	RPTEC	kidney:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
31	CTCF	chr12:49690360-49690510	AG10803	skin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
32	CTCF	chr12:49690340-49690631	MCF-7	breast:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
33	CTCF	chr12:49690420-49690570	K562	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
34	CTCF	chr12:49690380-49690530	K562	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
35	TBL1XR1	chr12:49690440-49690544	K562	blood:	n/a	n/a
36	MAX	chr12:49690104-49691625	MCF-7	breast:	n/a	n/a
37	CREB1	chr12:49690266-49690698	A549	lung:	n/a	n/a
38	CTCF	chr12:49690380-49690530	GM12874	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
39	ZBTB7A	chr12:49690083-49690882	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr12:49690400-49690550	AG09309	skin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
41	CTCF	chr12:49690344-49690655	Lung_OC	lung:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
42	CTCF	chr12:49690460-49690610	HFF-Myc	foreskin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
43	YY1	chr12:49690324-49690593	K562	blood:	n/a	chr12:49690476-49690485
44	CTCFL	chr12:49690364-49690574	K562	blood:	n/a	chr12:49690467-49690476
45	RAD21	chr12:49690339-49690601	K562	blood:	n/a	chr12:49690477-49690489 chr12:49690467-49690481 chr12:49690463-49690482 chr12:49690469-49690483
46	E2F4	chr12:49690449-49690573	MCF10A-Er-Src	breast:	n/a	chr12:49690476-49690485
47	CTCF	chr12:49690420-49690570	HFF-Myc	foreskin:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
48	CTCF	chr12:49690400-49690550	GM12869	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
49	CTCF	chr12:49690400-49690550	GM12873	blood:	n/a	chr12:49690470-49690483 chr12:49690467-49690480 chr12:49690465-49690483 chr12:49690466-49690482 chr12:49690460-49690481 chr12:49690467-49690480
50	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

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
ENSG00000186897	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000135451	Chromatin interaction

Extended variants
information (count: 52 )
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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12322798	1.00[ASN][1000 genomes]
rs12581343	0.85[ASN][1000 genomes]
rs12581428	0.93[ASN][1000 genomes]
rs12582657	0.92[AMR][1000 genomes]
rs2230550	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	1.00[AMR][1000 genomes];0.85[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]
rs57451017	0.85[EUR][1000 genomes];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: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:90 , 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	chr12:49687600-49690600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:49687600-49691000	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr12:49687600-49691000	Weak transcription	Hela-S3	cervix
6	chr12:49687800-49692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:49688200-49691400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
8	chr12:49688600-49691800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr12:49688800-49690600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
10	chr12:49688800-49690600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr12:49689000-49690600	Bivalent Enhancer	Primary B cells from cord blood	blood
12	chr12:49689000-49690600	Enhancers	Gastric	stomach
13	chr12:49689200-49690600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:49689200-49690600	Bivalent Enhancer	Esophagus	oesophagus
15	chr12:49689200-49690600	Bivalent Enhancer	NHEK	skin
16	chr12:49689200-49690800	Enhancers	Pancreas	Pancrea
17	chr12:49689200-49691400	Bivalent Enhancer	Liver	Liver
18	chr12:49689400-49690600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
19	chr12:49689400-49690600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:49689400-49690800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr12:49689600-49690600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:49689600-49690600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:49689600-49690600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:49689600-49690600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:49689600-49690600	Enhancers	Right Ventricle	heart
26	chr12:49689600-49692600	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr12:49689800-49690600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
28	chr12:49689800-49691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:49690000-49690600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:49690000-49690600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr12:49690000-49690800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:49690000-49690800	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
33	chr12:49690000-49691000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr12:49690200-49690600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
35	chr12:49690200-49690600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:49690200-49690600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
37	chr12:49690200-49690600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:49690200-49690600	Bivalent Enhancer	Brain Hippocampus Middle	brain
39	chr12:49690200-49690600	Bivalent Enhancer	Colon Smooth Muscle	Colon
40	chr12:49690200-49690600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
41	chr12:49690200-49690600	Bivalent Enhancer	HMEC	breast
42	chr12:49690200-49690800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
43	chr12:49690200-49691000	Bivalent Enhancer	Brain Substantia Nigra	brain
44	chr12:49690200-49691000	Bivalent Enhancer	Fetal Lung	lung
45	chr12:49690200-49691200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr12:49690200-49691200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
47	chr12:49690200-49691200	Flanking Active TSS	K562	blood
48	chr12:49690200-49691400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:49690200-49691400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
50	chr12:49690200-49691400	Bivalent Enhancer	Fetal Brain Male	brain

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