Variant report

Variant	rs12577111
Chromosome Location	chr11:66438074-66438075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66437106-66439399	U87	brain:	n/a	n/a
2	POLR2A	chr11:66437875-66438104	ProgFib	skin:	n/a	n/a
3	POLR2A	chr11:66437927-66438418	HepG2	liver:	n/a	n/a
4	NFATC1	chr11:66437708-66438112	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:66437102-66439211	U87	brain:	n/a	n/a
6	POLR2A	chr11:66437250-66438136	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr11:66437276-66438133	U87	brain:	n/a	n/a
8	POLR2A	chr11:66437983-66438734	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr11:66437006-66438462	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr11:66437828-66438192	K562	blood:	n/a	n/a
11	POLR2A	chr11:66437160-66438109	PANC-1	pancreas:	n/a	n/a
12	CEBPB	chr11:66437954-66438168	IMR90	lung:	n/a	n/a
13	POLR2A	chr11:66437697-66438227	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:66436972-66439009	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr11:66437142-66438850	MCF-7	breast:	n/a	n/a
16	POLR2A	chr11:66437244-66439240	K562	blood:	n/a	n/a
17	POLR2A	chr11:66432453-66439184	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr11:66437238-66438133	U87	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66433561..66435825-chr11:66436517..66438156,2	MCF-7	breast:
2	chr11:66405535..66407660-chr11:66437498..66439253,3	MCF-7	breast:
3	chr11:66429755..66432475-chr11:66437099..66438809,2	MCF-7	breast:
4	chr11:66233510..66236487-chr11:66437433..66439085,2	K562	blood:
5	chr11:66412064..66414929-chr11:66436700..66439361,2	K562	blood:
6	chr11:66434858..66442780-chr11:66443506..66446731,13	MCF-7	breast:
7	chr11:66422028..66424888-chr11:66437074..66439023,2	K562	blood:
8	chr11:66427413..66430054-chr11:66438064..66440207,2	MCF-7	breast:

No data

Variant related genes	Relation type
RBM4B	TF binding region
ENSG00000173914	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000258297	Chromatin interaction
ENSG00000174516	Chromatin interaction
ENSG00000173933	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12417769	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804382	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12805133	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs1671062	0.86[JPT][hapmap];0.86[MKK][hapmap]
rs1671063	0.81[JPT][hapmap];0.86[MKK][hapmap]
rs1671064	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs1791684	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs1815739	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs2276138	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279863	0.85[JPT][hapmap]
rs2513658	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs34900764	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3741363	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474602	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs477557	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs486584	0.90[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4930387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498045	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs503250	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs508443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs509556	0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs535211	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs540874	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs543191	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs556759	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs560556	0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs566673	0.85[CEU][hapmap]
rs569818	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs572846	0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs577023	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs577335	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs580910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs594313	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap]
rs608248	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs618838	0.83[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs627330	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs6591221	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs677488	0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs678397	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs682842	0.83[ASW][hapmap];0.82[MKK][hapmap]
rs692892	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs8432	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12577111	UNC93B1	cis	cerebellum	SCAN
rs12577111	BBS1	cis	cerebellum	SCAN
rs12577111	ACTN3	cis	Muscle Skeletal	GTEx
rs12577111	CCS	cis	lymphoblastoid	seeQTL
rs12577111	CCDC85B	cis	parietal	SCAN
rs12577111	CCS	cis	multi-tissue	Pritchard
rs12577111	CTSF	cis	parietal	SCAN
rs12577111	ACTN3	cis	lymphoblastoid	seeQTL
rs12577111	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs12577111	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs12577111	PRDX5	cis	cerebellum	SCAN
rs12577111	CDC42EP2	cis	cerebellum	SCAN
rs12577111	TRMT112	cis	cerebellum	SCAN
rs12577111	CTSF	cis	cerebellum	SCAN
rs12577111	YIF1A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66411800-66442800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66412000-66438800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:66413000-66440400	Strong transcription	Fetal Stomach	stomach
4	chr11:66413000-66442600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:66413400-66438400	Strong transcription	Dnd41	blood
6	chr11:66413600-66438400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:66414800-66442600	Weak transcription	Small Intestine	intestine
8	chr11:66415000-66438800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:66420000-66438400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:66420600-66443800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:66422200-66439400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:66422800-66438600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:66424000-66438800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:66424200-66438400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:66424200-66438600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:66424200-66439200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:66424400-66438800	Strong transcription	Fetal Intestine Large	intestine
18	chr11:66426000-66439200	Strong transcription	Primary T cells from cord blood	blood
19	chr11:66426800-66438800	Strong transcription	HSMM	muscle
20	chr11:66427600-66443200	Weak transcription	Stomach Mucosa	stomach
21	chr11:66428000-66438800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:66428000-66438800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:66428400-66438600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr11:66428400-66438600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:66428400-66438600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:66428400-66438800	Strong transcription	Hela-S3	cervix
27	chr11:66428600-66438400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr11:66430600-66438400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:66430800-66438800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:66432000-66438200	Strong transcription	Placenta	Placenta
31	chr11:66432000-66438600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr11:66432200-66438400	Strong transcription	K562	blood
33	chr11:66432200-66438800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:66432400-66438400	Strong transcription	A549	lung
35	chr11:66433400-66438800	Strong transcription	Primary B cells from cord blood	blood
36	chr11:66433600-66438200	Weak transcription	Fetal Heart	heart
37	chr11:66434000-66443800	Weak transcription	Colonic Mucosa	Colon
38	chr11:66434000-66444600	Weak transcription	Aorta	Aorta
39	chr11:66434400-66439400	Genic enhancers	Fetal Thymus	thymus
40	chr11:66434800-66442800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr11:66435000-66440400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:66435200-66440600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:66435400-66442600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:66435600-66440400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr11:66435800-66438600	Genic enhancers	Fetal Muscle Leg	muscle
46	chr11:66435800-66442400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:66436000-66443200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:66436000-66444400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr11:66436200-66438400	Weak transcription	NHDF-Ad	bronchial
50	chr11:66436200-66442400	Weak transcription	NH-A	brain

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