Variant report

Variant	rs627055
Chromosome Location	chr11:63889293-63889294
allele	C/T
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	GATA3	chr11:63888962-63889890	SK-N-SH	brain:	n/a	n/a
2	RCOR1	chr11:63888285-63890056	IMR90	lung:	n/a	n/a
3	MEF2A	chr11:63888925-63889875	SK-N-SH	brain:	n/a	chr11:63889583-63889604 chr11:63889588-63889602 chr11:63889329-63889340 chr11:63889590-63889599 chr11:63889587-63889603 chr11:63889587-63889602 chr11:63889589-63889600 chr11:63889583-63889604 chr11:63889583-63889604
4	FOS	chr11:63889210-63889451	MCF10A-Er-Src	breast:	n/a	n/a
5	RAD21	chr11:63888974-63889743	IMR90	lung:	n/a	n/a
6	TCF12	chr11:63888871-63889672	SK-N-SH	brain:	n/a	chr11:63889065-63889075
7	POLR2A	chr11:63889085-63889433	SK-N-SH	brain:	n/a	n/a
8	FOS	chr11:63889212-63889665	MCF10A-Er-Src	breast:	n/a	n/a
9	FOSL2	chr11:63888962-63889936	SK-N-SH	brain:	n/a	n/a
10	MAFK	chr11:63888951-63889610	IMR90	lung:	n/a	n/a
11	GATA3	chr11:63888971-63889901	SK-N-SH	brain:	n/a	n/a
12	MXI1	chr11:63888706-63889912	IMR90	lung:	n/a	n/a
13	RXRA	chr11:63888978-63889652	SK-N-SH	brain:	n/a	chr11:63889608-63889617

No.	Distal block	Cell Line	Cell type
1	chr11:63888452..63890195-chr11:63909642..63911388,2	K562	blood:
2	chr11:63889039..63891397-chr11:63901095..63904442,4	K562	blood:
3	chr11:63888646..63891541-chr11:63955037..63956555,2	MCF-7	breast:
4	chr11:63888929..63891222-chr11:63896109..63898759,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256341	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10897474	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11231704	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11231741	0.84[JPT][hapmap]
rs1123251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787945	0.81[CEU][hapmap]
rs1317494	1.00[JPT][hapmap]
rs2186643	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2236647	0.85[CEU][hapmap];0.98[GIH][hapmap]
rs2236648	0.81[CEU][hapmap]
rs2325786	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2325787	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2875748	0.85[CEU][hapmap];0.98[GIH][hapmap]
rs3815362	0.84[JPT][hapmap]
rs4930152	0.84[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs4980508	0.95[GIH][hapmap]
rs4980524	0.81[CEU][hapmap]
rs4980525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55970722	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7938819	0.85[CEU][hapmap]
rs882147	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	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
7	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs627055	TRMT112	cis	parietal	SCAN
rs627055	PRDX5	cis	parietal	SCAN
rs627055	MRPL49	cis	cerebellum	SCAN
rs627055	FRMD8	cis	cerebellum	SCAN
rs627055	BATF2	cis	cerebellum	SCAN
rs627055	FKBP2	cis	parietal	SCAN
rs627055	FKBP2	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63875400-63896200	Weak transcription	Spleen	Spleen
2	chr11:63879600-63890200	Weak transcription	Liver	Liver
3	chr11:63879800-63891600	Weak transcription	Primary T cells from cord blood	blood
4	chr11:63881800-63891800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:63882200-63889400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:63882200-63889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:63882200-63889600	Weak transcription	Lung	lung
8	chr11:63882200-63892800	Weak transcription	Fetal Kidney	kidney
9	chr11:63883000-63890800	Weak transcription	Dnd41	blood
10	chr11:63884600-63889800	Weak transcription	Pancreas	Pancrea
11	chr11:63885000-63896600	Weak transcription	Hela-S3	cervix
12	chr11:63885400-63889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:63885400-63892400	Weak transcription	Fetal Intestine Small	intestine
14	chr11:63885400-63898600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:63885600-63911200	Weak transcription	Gastric	stomach
16	chr11:63886000-63891000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:63886000-63891200	Enhancers	Fetal Brain Male	brain
18	chr11:63886200-63890800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:63886200-63890800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:63886800-63908600	Weak transcription	Ovary	ovary
21	chr11:63887200-63892000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr11:63887400-63890800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:63887600-63890800	Enhancers	Brain Cingulate Gyrus	brain
24	chr11:63887800-63890400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr11:63887800-63891000	Enhancers	Brain Germinal Matrix	brain
26	chr11:63888000-63890400	Enhancers	HMEC	breast
27	chr11:63888000-63890800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr11:63888000-63891000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:63888000-63891800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr11:63888000-63891800	Enhancers	Fetal Muscle Leg	muscle
31	chr11:63888200-63889400	Enhancers	Esophagus	oesophagus
32	chr11:63888200-63890000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:63888200-63890000	Enhancers	Brain Angular Gyrus	brain
34	chr11:63888200-63890200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:63888200-63890400	Enhancers	HSMMtube	muscle
36	chr11:63888200-63890600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:63888200-63890600	Enhancers	HSMM	muscle
38	chr11:63888200-63890800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:63888200-63890800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:63888200-63891600	Enhancers	Brain Anterior Caudate	brain
41	chr11:63888200-63891800	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr11:63888200-63892000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:63888200-63894000	Enhancers	Fetal Thymus	thymus
44	chr11:63888400-63889400	Enhancers	Brain Substantia Nigra	brain
45	chr11:63888400-63889800	Enhancers	Fetal Stomach	stomach
46	chr11:63888400-63890000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:63888400-63890200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:63888400-63890200	Enhancers	Muscle Satellite Cultured Cells	--
49	chr11:63888400-63890400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr11:63888400-63890400	Enhancers	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links