Variant report

Variant	rs11052282
Chromosome Location	chr12:9820080-9820081
allele	A/C
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	POLR2A	chr12:9819935-9822633	GM12891	blood:	n/a	n/a
2	ATF2	chr12:9819851-9820465	GM12878	blood:	n/a	n/a
3	RUNX3	chr12:9819837-9820412	GM12878	blood:	n/a	n/a
4	CTCF	chr12:9819980-9820130	GM12872	blood:	n/a	n/a
5	BHLHE40	chr12:9819899-9820357	GM12878	blood:	n/a	n/a
6	STAT3	chr12:9820043-9820139	GM12878	blood:	n/a	n/a
7	ZNF384	chr12:9819946-9820458	GM12878	blood:	n/a	n/a
8	EP300	chr12:9819868-9820595	GM12878	blood:	n/a	n/a
9	FOXM1	chr12:9819909-9820404	GM12878	blood:	n/a	n/a
10	TBP	chr12:9820004-9820427	GM12878	blood:	n/a	n/a
11	CTCF	chr12:9819960-9820110	GM12865	blood:	n/a	n/a
12	TBL1XR1	chr12:9819879-9820528	GM12878	blood:	n/a	n/a
13	EP300	chr12:9819928-9820384	GM12878	blood:	n/a	n/a
14	CTCF	chr12:9820060-9820210	GM12872	blood:	n/a	n/a
15	CHD1	chr12:9819935-9820676	GM12878	blood:	n/a	n/a
16	RFX5	chr12:9820015-9820248	GM12878	blood:	n/a	n/a
17	RCOR1	chr12:9819980-9820555	GM12878	blood:	n/a	n/a
18	CUX1	chr12:9819957-9820466	GM12878	blood:	n/a	n/a
19	EBF1	chr12:9819959-9820354	GM12878	blood:	n/a	n/a
20	NFIC	chr12:9819870-9820734	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9815292..9817127-chr12:9818651..9820715,3	MCF-7	breast:

Variant related genes	Relation type
CLEC2D	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10466762	0.89[ASN][1000 genomes]
rs10772005	0.89[ASN][1000 genomes]
rs10772006	0.89[ASN][1000 genomes]
rs10844236	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10844267	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10844327	0.89[ASN][1000 genomes]
rs10844350	0.89[ASN][1000 genomes]
rs10844351	0.89[ASN][1000 genomes]
rs10844352	0.89[ASN][1000 genomes]
rs10844353	0.89[ASN][1000 genomes]
rs10844359	0.89[ASN][1000 genomes]
rs11052207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052235	0.89[ASN][1000 genomes]
rs11052245	0.89[ASN][1000 genomes]
rs11052254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11608817	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12310789	0.89[ASN][1000 genomes]
rs12366653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12366792	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12809846	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12820641	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12830419	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12831287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1560008	0.89[ASN][1000 genomes]
rs16913477	0.89[ASN][1000 genomes]
rs1863871	0.89[ASN][1000 genomes]
rs2114869	0.89[ASN][1000 genomes]
rs2162657	0.89[ASN][1000 genomes]
rs34323946	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34833649	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34981673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015427	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35098654	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35280686	0.89[ASN][1000 genomes]
rs35561167	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35642909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35671537	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35884213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55873283	0.89[ASN][1000 genomes]
rs61916061	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7132037	0.89[ASN][1000 genomes]
rs7136821	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7299738	0.89[ASN][1000 genomes]
rs7302110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302746	0.89[ASN][1000 genomes]
rs7304321	0.89[ASN][1000 genomes]
rs7304464	0.89[ASN][1000 genomes]
rs7305937	0.89[ASN][1000 genomes]
rs7309800	0.89[ASN][1000 genomes]
rs7310405	0.89[ASN][1000 genomes]
rs7310516	0.89[ASN][1000 genomes]
rs7310568	0.89[ASN][1000 genomes]
rs7310790	0.89[ASN][1000 genomes]
rs7311421	0.89[ASN][1000 genomes]
rs7311574	0.89[ASN][1000 genomes]
rs7311945	0.89[ASN][1000 genomes]
rs7959406	0.89[ASN][1000 genomes]
rs7959726	0.89[ASN][1000 genomes]
rs7961262	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962321	0.89[ASN][1000 genomes]
rs7967102	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7973603	0.89[ASN][1000 genomes]
rs7974871	0.89[ASN][1000 genomes]
rs7978187	0.89[ASN][1000 genomes]
rs958340	0.89[ASN][1000 genomes]
rs9919786	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11052282	RP11-705C15.3	cis	Whole Blood	GTEx
rs11052282	RP11-705C15.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11052282	CLEC2D	cis	Esophagus Muscularis	GTEx
rs11052282	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
3	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
4	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
5	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
6	chr12:9804600-9820200	Weak transcription	NHEK	skin
7	chr12:9806200-9821600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:9807000-9826000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:9812000-9820400	Weak transcription	NHLF	lung
11	chr12:9812800-9825800	Weak transcription	Right Ventricle	heart
12	chr12:9813000-9825800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:9813000-9826200	Weak transcription	Brain Anterior Caudate	brain
14	chr12:9813000-9826200	Weak transcription	Gastric	stomach
15	chr12:9813800-9826000	Weak transcription	NHDF-Ad	bronchial
16	chr12:9815000-9820200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9815000-9820800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:9815000-9822400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:9815000-9826000	Weak transcription	Lung	lung
20	chr12:9815000-9826000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:9815000-9826200	Weak transcription	Colonic Mucosa	Colon
22	chr12:9815000-9826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:9815000-9826400	Weak transcription	Fetal Intestine Small	intestine
24	chr12:9815200-9820200	Weak transcription	NH-A	brain
25	chr12:9815200-9824000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:9815200-9825000	Weak transcription	K562	blood
27	chr12:9815200-9825800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:9815200-9825800	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:9815200-9826200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr12:9815200-9828400	Weak transcription	Liver	Liver
31	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
32	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
33	chr12:9815400-9825000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:9815400-9825600	Weak transcription	HepG2	liver
35	chr12:9815600-9825200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:9815600-9825600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:9815600-9825800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:9815600-9826000	Weak transcription	Spleen	Spleen
39	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:9815800-9825600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:9817000-9826000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:9817200-9820600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:9817200-9824800	Weak transcription	Dnd41	blood
46	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
47	chr12:9817600-9820200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:9817600-9825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:9817600-9826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:9818000-9820400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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