Variant report

Variant	rs12787945
Chromosome Location	chr11:63977546-63977547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:63977313-63977824	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:63977270-63978370	GM12892	blood:	n/a	n/a
3	HEY1	chr11:63977363-63977635	K562	blood:	n/a	n/a
4	POLR2A	chr11:63972968-63979020	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:63972869-63978649	K562	blood:	n/a	n/a
6	POLR2A	chr11:63972937-63980346	K562	blood:	n/a	n/a
7	POLR2A	chr11:63971678-63979009	K562	blood:	n/a	n/a
8	POLR2A	chr11:63976338-63978616	GM12892	blood:	n/a	n/a
9	POLR2A	chr11:63973003-63978509	GM18505	blood:	n/a	n/a
10	POLR2A	chr11:63977325-63978022	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:63973075-63978498	K562	blood:	n/a	n/a
12	POLR2A	chr11:63977326-63977557	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:63971863-63978624	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:63977271-63978009	GM12891	blood:	n/a	n/a
15	POLR2A	chr11:63972934-63978589	K562	blood:	n/a	n/a
16	POLR2A	chr11:63977358-63978228	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:63972993-63978500	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:63977088-63977753	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr11:63972863-63978613	GM12892	blood:	n/a	n/a
20	POLR2A	chr11:63976389-63978613	HL-60	blood:	n/a	n/a
21	POLR2A	chr11:63972927-63977931	GM12891	blood:	n/a	n/a
22	POLR2A	chr11:63973077-63978637	K562	blood:	n/a	n/a
23	POLR2A	chr11:63977464-63977564	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr11:63977134-63978399	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63972047..63977847-chr11:64122012..64128099,8	K562	blood:
2	chr11:63975945..63977669-chr2:60461568..60463087,2	K562	blood:
3	chr11:63969363..63977705-chr11:64080619..64088284,16	K562	blood:
4	chr11:63976736..63978264-chr11:63980722..63982824,2	MCF-7	breast:
5	chr11:63974393..63980083-chr11:64051080..64055862,5	MCF-7	breast:
6	chr11:63975807..63978455-chr11:64073028..64075602,2	MCF-7	breast:
7	chr11:63972384..63977847-chr11:64121311..64126015,8	K562	blood:

No data

Variant related genes	Relation type
FERMT3	TF binding region
ENSG00000168071	Chromatin interaction
ENSG00000126432	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000002330	Chromatin interaction
ENSG00000173264	Chromatin interaction
ENSG00000173113	Chromatin interaction
ENSG00000162302	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11231722	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603042	0.80[CHD][hapmap]
rs11603192	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs11603384	0.87[CHD][hapmap]
rs11603538	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs12362602	0.87[EUR][1000 genomes]
rs12418535	0.80[CHB][hapmap]
rs17699798	0.86[EUR][1000 genomes]
rs1860368	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2236647	0.96[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2236648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282492	0.80[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs2429455	0.81[ASW][hapmap];0.83[CHD][hapmap];0.85[LWK][hapmap];0.87[YRI][hapmap]
rs2515241	0.80[CHB][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2701533	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2845597	0.93[ASW][hapmap];0.80[CHB][hapmap];0.90[CHD][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes]
rs2875748	0.88[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs4980508	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs4980524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4980525	0.85[CEU][hapmap]
rs594942	0.87[ASW][hapmap];0.87[YRI][hapmap]
rs604203	0.83[CHD][hapmap]
rs60452247	0.80[ASN][1000 genomes]
rs627055	0.81[CEU][hapmap]
rs645461	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7112960	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs7938819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7948329	0.90[EUR][1000 genomes]
rs882147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
6	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
7	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
8	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
9	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
10	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats 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	166 gene(s)	inside rSNPs	diseases
11	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
12	nsv897665	chr11:63927695-64026144	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
13	nsv897666	chr11:63929493-64026144	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	155 gene(s)	inside rSNPs	diseases
14	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
15	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
16	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
17	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
18	nsv468595	chr11:63953121-64027888	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
19	nsv555187	chr11:63953121-64027888	Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases
20	nsv897667	chr11:63964657-64078380	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
21	nsv897668	chr11:63964657-64085298	Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
22	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
23	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
24	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
25	nsv541061	chr11:63970174-64010995	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
26	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12787945	PRDX5	cis	parietal	SCAN
rs12787945	FKBP2	cis	parietal	SCAN
rs12787945	TRMT112	cis	parietal	SCAN
rs12787945	MRPL49	cis	cerebellum	SCAN
rs12787945	FKBP2	cis	cerebellum	SCAN
rs12787945	NUDT22	cis	lymphoblastoid	seeQTL
rs12787945	MALAT1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63970200-63979000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:63971600-63992800	Weak transcription	Fetal Kidney	kidney
3	chr11:63972000-63980000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:63972000-63990000	Weak transcription	Ovary	ovary
5	chr11:63973200-63978600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:63973200-63987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:63973400-63983000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:63973600-63993000	Weak transcription	Aorta	Aorta
9	chr11:63973800-63982600	Weak transcription	Hela-S3	cervix
10	chr11:63974000-63986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:63974200-63982400	Weak transcription	HMEC	breast
12	chr11:63974400-63986200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:63974800-63987600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:63975000-63986000	Weak transcription	NHEK	skin
15	chr11:63975000-63986200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:63975000-63988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:63975200-63978000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:63975200-63979200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:63975200-63992600	Weak transcription	Brain Angular Gyrus	brain
20	chr11:63975400-63979000	Weak transcription	Liver	Liver
21	chr11:63975400-63982600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:63975400-63985200	Weak transcription	Pancreas	Pancrea
23	chr11:63975400-63986400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:63975400-63990200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:63975600-63979200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:63975600-63980200	Strong transcription	Gastric	stomach
27	chr11:63975600-63987000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:63975600-63992400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:63975600-63992600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:63975600-63992600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:63975600-63992800	Weak transcription	Fetal Lung	lung
32	chr11:63975800-63977800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:63975800-63977800	Enhancers	Fetal Muscle Leg	muscle
34	chr11:63975800-63988000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:63975800-63990200	Weak transcription	Psoas Muscle	Psoas
36	chr11:63975800-63990400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:63975800-63992400	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:63975800-63992600	Weak transcription	Left Ventricle	heart
39	chr11:63975800-63992600	Weak transcription	Osteobl	bone
40	chr11:63975800-63993000	Weak transcription	Small Intestine	intestine
41	chr11:63976000-63977600	Weak transcription	Fetal Intestine Large	intestine
42	chr11:63976000-63977800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr11:63976000-63977800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:63976000-63977800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:63976000-63978000	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr11:63976000-63978200	Weak transcription	Fetal Brain Female	brain
47	chr11:63976000-63979000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:63976000-63979600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr11:63976000-63982400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:63976200-63977600	Enhancers	Brain Hippocampus Middle	brain

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