Variant report

Variant	rs2012773
Chromosome Location	chr12:48591399-48591400
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:183)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:183 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr12:48591330-48592637	GM12878	blood:	n/a	n/a
2	CTCF	chr12:48591280-48591430	GM12875	blood:	n/a	n/a
3	CEBPB	chr12:48591338-48591636	K562	blood:	n/a	n/a
4	ZNF143	chr12:48591328-48591609	K562	blood:	n/a	n/a
5	CUX1	chr12:48591336-48592190	K562	blood:	n/a	n/a
6	KAP1	chr12:48591333-48591675	K562	blood:	n/a	n/a
7	CTCF	chr12:48591288-48591534	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr12:48591320-48591470	BE2_C	brain:	n/a	n/a
9	RAD21	chr12:48591194-48591552	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr12:48591195-48591624	A549	lung:	n/a	n/a
11	TEAD4	chr12:48591248-48592854	K562	blood:	n/a	n/a
12	MAX	chr12:48591206-48592554	ECC-1	luminal epithelium:	n/a	n/a
13	RAD21	chr12:48591266-48592332	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr12:48591340-48591490	GM12871	blood:	n/a	n/a
15	CTCF	chr12:48591174-48591676	MCF-7	breast:	n/a	n/a
16	CTCF	chr12:48591360-48591510	HPF	lung:	n/a	n/a
17	CTCF	chr12:48591360-48591510	AG04449	skin:	n/a	n/a
18	CTCF	chr12:48591380-48591530	HEK293	kidney:	n/a	n/a
19	CTCF	chr12:48591338-48591536	Pancreas_OC	pancreas:	n/a	n/a
20	RCOR1	chr12:48591318-48592282	K562	blood:	n/a	n/a
21	TBP	chr12:48591392-48592699	GM12878	blood:	n/a	n/a
22	CTCF	chr12:48591380-48591530	HMF	breast:	n/a	n/a
23	CTCF	chr12:48591323-48591581	K562	blood:	n/a	n/a
24	CTCF	chr12:48591300-48591450	NHDF-neo	bronchial:	n/a	n/a
25	CTCF	chr12:48591340-48591490	HPF	lung:	n/a	n/a
26	CTCF	chr12:48591360-48591510	SAEC	small airway:	n/a	n/a
27	CTCF	chr12:48591241-48592366	K562	blood:	n/a	n/a
28	SIN3A	chr12:48591211-48592583	H1-hESC	embryonic stem cell:	n/a	chr12:48591416-48591424
29	CTCF	chr12:48591360-48591510	AG09319	gingival:	n/a	n/a
30	CTCF	chr12:48591305-48591674	Spleen_OC	spleen:	n/a	n/a
31	CTCF	chr12:48591295-48591619	HUVEC	blood vessel:	n/a	n/a
32	MAX	chr12:48591309-48592797	A549	lung:	n/a	n/a
33	CTCF	chr12:48591320-48591470	GM06990	blood:	n/a	n/a
34	MAFK	chr12:48591262-48592101	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr12:48591332-48591546	GM13977	blood:	n/a	n/a
36	RAD21	chr12:48591297-48591566	GM12878	blood:	n/a	n/a
37	CTCF	chr12:48591300-48591450	BJ	skin:	n/a	n/a
38	CTCF	chr12:48591340-48591490	GM12869	blood:	n/a	n/a
39	CTCF	chr12:48591300-48591450	AG04450	lung:	n/a	n/a
40	KAP1	chr12:48591024-48592633	HEK293	kidney:	n/a	n/a
41	CTCF	chr12:48591340-48591490	GM12874	blood:	n/a	n/a
42	CTCF	chr12:48591331-48591623	Lung_OC	lung:	n/a	n/a
43	SP1	chr12:48591266-48592436	A549	lung:	n/a	n/a
44	CTCF	chr12:48591320-48591470	HCPEpiC	choroid plexus:	n/a	n/a
45	CTCF	chr12:48591321-48591587	GM10266	blood:	n/a	n/a
46	CTCF	chr12:48591320-48591470	GM12865	blood:	n/a	n/a
47	CTCF	chr12:48591320-48591470	Hela-S3	cervix:	n/a	n/a
48	STAT5A	chr12:48591385-48592740	GM12878	blood:	n/a	n/a
49	CTCF	chr12:48591366-48591483	MCF-7	breast:	n/a	n/a
50	CTCF	chr12:48591380-48591530	GM12867	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48583311..48584177-chr12:48591097..48592094,2	K562	blood:
2	chr12:48549910..48551454-chr12:48590661..48592818,2	K562	blood:
3	chr12:48582333..48583154-chr12:48590725..48591457,2	K562	blood:
4	chr12:48549661..48552655-chr12:48590661..48593368,4	K562	blood:
5	chr12:48589603..48591970-chr12:48853785..48856420,2	MCF-7	breast:
6	chr12:48590039..48593666-chr12:48742360..48744824,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269514	TF binding region
ENSG00000167528	Chromatin interaction
ENSG00000257735	Chromatin interaction
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10082861	1.00[JPT][hapmap]
rs1021313	0.83[ASN][1000 genomes]
rs10219623	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10437919	0.83[ASN][1000 genomes]
rs10437920	0.83[ASN][1000 genomes]
rs10467101	0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10783234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875724	0.93[JPT][hapmap]
rs10875725	1.00[JPT][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875745	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10875746	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10875750	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10875756	0.84[ASN][1000 genomes]
rs10875762	0.92[ASN][1000 genomes]
rs10875764	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875767	0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10875768	0.85[ASN][1000 genomes]
rs10875769	0.88[ASN][1000 genomes]
rs10875770	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10875772	0.84[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10875777	0.83[ASN][1000 genomes]
rs10875778	0.83[ASN][1000 genomes]
rs10875779	0.83[ASN][1000 genomes]
rs10875782	0.80[ASN][1000 genomes]
rs10875792	0.85[JPT][hapmap]
rs10875793	0.92[JPT][hapmap]
rs11168357	0.93[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	1.00[JPT][hapmap]
rs11168403	1.00[JPT][hapmap]
rs11168413	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168414	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11168418	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11168420	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168421	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168425	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168427	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11168433	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168459	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168483	0.80[ASN][1000 genomes]
rs11168487	0.83[ASN][1000 genomes]
rs11168516	0.87[JPT][hapmap]
rs11558768	0.91[ASN][1000 genomes]
rs12297470	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12300647	0.80[ASN][1000 genomes]
rs12304476	1.00[JPT][hapmap]
rs12305182	0.93[JPT][hapmap]
rs12305511	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12305647	0.94[ASN][1000 genomes]
rs12306451	1.00[JPT][hapmap]
rs12310813	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12312134	0.89[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs12317751	0.83[ASN][1000 genomes]
rs12318705	0.80[ASN][1000 genomes]
rs1471997	0.86[JPT][hapmap]
rs17122666	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs17122812	0.84[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1859445	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2079295	0.93[JPT][hapmap]
rs2107638	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2171642	0.80[ASN][1000 genomes]
rs2228500	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2269933	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2269935	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.87[JPT][hapmap]
rs2634675	0.87[JPT][hapmap]
rs2732439	0.87[JPT][hapmap]
rs2732465	0.87[JPT][hapmap]
rs2898065	0.82[ASN][1000 genomes]
rs3185921	0.87[JPT][hapmap]
rs3751273	0.87[JPT][hapmap]
rs3782910	1.00[JPT][hapmap]
rs4760609	0.93[JPT][hapmap]
rs4760619	1.00[JPT][hapmap]
rs4760622	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760681	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4760687	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4760689	0.84[ASN][1000 genomes]
rs4760690	0.84[ASN][1000 genomes]
rs4760695	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4760696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760699	0.85[ASN][1000 genomes]
rs61940962	0.86[ASN][1000 genomes]
rs61941003	0.83[ASN][1000 genomes]
rs61941006	0.83[ASN][1000 genomes]
rs6580659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716553	0.83[ASN][1000 genomes]
rs719008	0.93[JPT][hapmap]
rs725454	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs7302466	0.80[ASN][1000 genomes]
rs7303055	0.83[ASN][1000 genomes]
rs7486008	0.83[ASN][1000 genomes]
rs7486424	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7975956	0.80[ASN][1000 genomes]
rs8804	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs886588	1.00[JPT][hapmap]
rs9634261	0.87[JPT][hapmap]
rs989144	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2012773	ZNF641	cis	Muscle Skeletal	GTEx
rs2012773	ZNF641	cis	Whole Blood	GTEx
rs2012773	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48585800-48591400	Weak transcription	Esophagus	oesophagus
2	chr12:48589000-48591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48590800-48591400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr12:48590800-48591400	Flanking Active TSS	A549	lung
5	chr12:48590800-48591600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:48590800-48592400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:48590800-48592600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48590800-48593000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr12:48591000-48591400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr12:48591000-48591400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:48591000-48591400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
12	chr12:48591000-48591400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:48591000-48591400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:48591000-48591400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48591000-48591400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:48591000-48591400	Enhancers	Primary B cells from peripheral blood	blood
17	chr12:48591000-48591400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:48591000-48591400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:48591000-48591400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:48591000-48591400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:48591000-48591400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:48591000-48591400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:48591000-48591400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:48591000-48591400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr12:48591000-48591400	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:48591000-48591400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:48591000-48591400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:48591000-48591400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:48591000-48591400	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr12:48591000-48591400	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr12:48591000-48591400	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr12:48591000-48591400	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr12:48591000-48591400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr12:48591000-48591400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:48591000-48591400	Flanking Active TSS	Fetal Brain Female	brain
36	chr12:48591000-48591400	Enhancers	Fetal Heart	heart
37	chr12:48591000-48591400	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr12:48591000-48591400	Flanking Active TSS	Fetal Kidney	kidney
39	chr12:48591000-48591400	Enhancers	Fetal Muscle Leg	muscle
40	chr12:48591000-48591400	Flanking Active TSS	Placenta	Placenta
41	chr12:48591000-48591400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:48591000-48591600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr12:48591000-48591800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr12:48591000-48591800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr12:48591000-48591800	Flanking Active TSS	NH-A	brain
46	chr12:48591000-48591800	Flanking Active TSS	NHEK	skin
47	chr12:48591000-48592000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr12:48591000-48592000	Flanking Active TSS	GM12878-XiMat	blood
49	chr12:48591000-48592000	Flanking Active TSS	HMEC	breast
50	chr12:48591000-48592000	Flanking Active TSS	K562	blood

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