Variant report

Variant	rs11168839
Chromosome Location	chr12:49457635-49457636
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	chr12:49457452-49457979	H1-hESC	embryonic stem cell:	n/a	chr12:49457620-49457630
2	SMC3	chr12:49457475-49458314	SK-N-SH	brain:	n/a	chr12:49457881-49457895
3	MXI1	chr12:49457013-49458246	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr12:49457567-49458172	MCF-7	breast:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
5	CTCF	chr12:49457579-49458087	A549	lung:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
6	CTCF	chr12:49457376-49458390	SK-N-SH	brain:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
7	CTCF	chr12:49457631-49458083	T-47D	breast:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
8	CBX3	chr12:49457623-49458118	K562	blood:	n/a	n/a
9	RAD21	chr12:49457618-49458072	SK-N-SH_RA	brain:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
10	CTCF	chr12:49457576-49458144	HCT-116	colon:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
11	CTCF	chr12:49457592-49458189	MCF-7	breast:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
12	RAD21	chr12:49457490-49458306	HCT-116	colon:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
13	ZC3H11A	chr12:49457623-49457961	K562	blood:	n/a	n/a
14	CTCF	chr12:49457293-49458337	HCT-116	colon:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
15	YY1	chr12:49457552-49457956	K562	blood:	n/a	chr12:49457620-49457630
16	POLR2A	chr12:49457597-49458123	PFSK-1	brain:	n/a	n/a
17	YY1	chr12:49457395-49457993	GM12878	blood:	n/a	chr12:49457620-49457630
18	FOXA2	chr12:49457610-49458035	A549	lung:	n/a	n/a
19	YY1	chr12:49457434-49457955	K562	blood:	n/a	chr12:49457620-49457630
20	YY1	chr12:49457453-49458081	H1-hESC	embryonic stem cell:	n/a	chr12:49457620-49457630
21	RFX5	chr12:49457602-49457768	HepG2	liver:	n/a	n/a
22	YY1	chr12:49457468-49457995	GM12891	blood:	n/a	chr12:49457620-49457630
23	FOSL2	chr12:49457442-49458116	A549	lung:	n/a	n/a
24	YY1	chr12:49457436-49458025	SK-N-SH_RA	brain:	n/a	chr12:49457620-49457630
25	ATF2	chr12:49457592-49458053	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAFF	chr12:49457580-49458050	K562	blood:	n/a	chr12:49457857-49457875
27	EP300	chr12:49457435-49458031	K562	blood:	n/a	n/a
28	RAD21	chr12:49457450-49458175	SK-N-SH	brain:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
29	POLR2A	chr12:49457606-49458098	K562	blood:	n/a	n/a
30	MAFK	chr12:49457569-49458086	Hela-S3	cervix:	n/a	chr12:49457858-49457874 chr12:49457858-49457873
31	RAD21	chr12:49457604-49458155	ECC-1	luminal epithelium:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
32	YY1	chr12:49457539-49458032	A549	lung:	n/a	chr12:49457620-49457630
33	RAD21	chr12:49457610-49458165	MCF-7	breast:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
34	RAD21	chr12:49457551-49458230	HCT-116	colon:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
35	CTCF	chr12:49456945-49458313	A549	lung:	n/a	chr12:49457880-49457896 chr12:49457882-49457895 chr12:49457884-49457892 chr12:49457881-49457902 chr12:49457879-49457897
36	MAFF	chr12:49457535-49458048	HepG2	liver:	n/a	chr12:49457857-49457875
37	MAFK	chr12:49457630-49458050	HepG2	liver:	n/a	chr12:49457858-49457874 chr12:49457858-49457873
38	MAFK	chr12:49457622-49458059	K562	blood:	n/a	chr12:49457858-49457874 chr12:49457858-49457873
39	RAD21	chr12:49457624-49458152	HepG2	liver:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
40	RAD21	chr12:49457556-49458200	A549	lung:	n/a	chr12:49457880-49457899 chr12:49457882-49457889 chr12:49457881-49457895
41	YY1	chr12:49457434-49457997	GM12878	blood:	n/a	chr12:49457620-49457630

No.	Distal block	Cell Line	Cell type
1	chr12:49447251..49459518-chr12:49480338..49487981,17	K562	blood:
2	chr12:49446392..49469923-chr12:49518127..49527853,66	K562	blood:
3	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
4	chr12:49455381..49457675-chr12:49576315..49579055,2	MCF-7	breast:
5	chr12:49457471..49458423-chr12:49482053..49483278,5	MCF-7	breast:
6	chr12:49457447..49458330-chr12:49514978..49515610,3	MCF-7	breast:
7	chr12:49455426..49457775-chr12:49666001..49667624,2	MCF-7	breast:
8	chr12:49457393..49458384-chr12:49481950..49482791,5	K562	blood:
9	chr12:49456178..49460565-chr12:49463551..49467043,4	MCF-7	breast:
10	chr12:49452588..49458658-chr12:49486666..49491439,6	MCF-7	breast:
11	chr12:49448896..49462070-chr12:49656751..49663992,28	K562	blood:
12	chr12:49451508..49465481-chr12:49521303..49528986,40	MCF-7	breast:
13	chr12:49457413..49458369-chr12:49491480..49492485,6	K562	blood:
14	chr12:49457477..49459224-chr12:49518339..49520842,2	MCF-7	breast:
15	chr12:49450455..49459531-chr12:49522374..49527837,16	MCF-7	breast:
16	chr12:49440399..49469923-chr12:49518291..49528303,83	K562	blood:
17	chr12:49453076..49457977-chr12:49485062..49491403,12	K562	blood:
18	chr12:49457385..49458293-chr12:49689998..49690907,2	K562	blood:
19	chr12:49457538..49458313-chr12:49485593..49486183,3	MCF-7	breast:
20	chr12:49457476..49458370-chr12:49491458..49492463,5	MCF-7	breast:
21	chr12:49449335..49458365-chr12:49656751..49666981,25	K562	blood:
22	chr12:49457494..49458333-chr12:49514684..49515283,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WNT1-3	chr12:49457155-49457826	XLOC_009740
2	lnc-WNT1-3	chr12:49457154-49457826	NONHSAT028067

Variant related genes	Relation type
KMT2D	TF binding region
ENSG00000258101	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258232	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000139549	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10459221	0.96[ASN][1000 genomes]
rs10459232	0.81[CEU][hapmap];0.96[ASN][1000 genomes]
rs1054442	0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10747559	0.82[AFR][1000 genomes]
rs10783299	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783300	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10783301	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10875908	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875910	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10875911	0.85[ASN][1000 genomes]
rs10875912	0.83[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10875913	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875914	0.84[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875915	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875917	0.96[ASN][1000 genomes]
rs10875918	0.95[ASN][1000 genomes]
rs11168822	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168827	1.00[CEU][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168838	0.99[ASN][1000 genomes]
rs11168850	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1138908	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11614738	0.84[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12298884	0.91[ASN][1000 genomes]
rs12580349	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12821008	0.95[ASN][1000 genomes]
rs2117029	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241726	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293445	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2293446	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304275	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34436857	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3741619	0.89[ASW][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3741622	0.91[JPT][hapmap]
rs3782357	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580698	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs6580699	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs7296288	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs7300136	0.95[ASN][1000 genomes]
rs7969091	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs876333	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11168839	RP11-386G11.3	cis	Muscle Skeletal	GTEx
rs11168839	RP11-386G11.5	cis	Muscle Skeletal	GTEx
rs11168839	DDN	cis	Muscle Skeletal	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49455200-49458600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:49455200-49461800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:49455200-49462800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:49455200-49462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:49455400-49458000	Weak transcription	Fetal Intestine Large	intestine
6	chr12:49455400-49458400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:49455400-49458600	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:49455400-49458600	Weak transcription	Thymus	Thymus
9	chr12:49455400-49458600	Weak transcription	Spleen	Spleen
10	chr12:49455400-49460200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:49455400-49461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:49455400-49461800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:49455400-49462600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:49455400-49462600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:49455400-49462600	Weak transcription	Primary T cells from cord blood	blood
16	chr12:49455400-49462600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:49455400-49462600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:49455400-49462600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:49455400-49462600	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:49455400-49462800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:49455400-49462800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:49455400-49462800	Weak transcription	Fetal Lung	lung
23	chr12:49455400-49462800	Weak transcription	Right Ventricle	heart
24	chr12:49455400-49462800	Weak transcription	HSMM	muscle
25	chr12:49455400-49463000	Weak transcription	Lung	lung
26	chr12:49455400-49463200	Weak transcription	Aorta	Aorta
27	chr12:49455600-49457800	Weak transcription	Liver	Liver
28	chr12:49455600-49457800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:49455600-49458600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:49455600-49459800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:49455600-49460200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:49455600-49461800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:49455600-49462400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:49455600-49462400	Weak transcription	GM12878-XiMat	blood
35	chr12:49455600-49462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:49455600-49462600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:49455600-49462600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:49455600-49462600	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:49455600-49462600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:49455600-49462600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:49455600-49462600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:49455600-49462600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:49455600-49462600	Weak transcription	Fetal Thymus	thymus
44	chr12:49455600-49462600	Weak transcription	HMEC	breast
45	chr12:49455600-49462600	Weak transcription	HUVEC	blood vessel
46	chr12:49455600-49462600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:49455600-49462600	Weak transcription	NH-A	brain
48	chr12:49455600-49462800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:49455600-49462800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:49455600-49462800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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