Variant report

Variant	rs11227624
Chromosome Location	chr11:66682860-66682861
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	POLR2A	chr11:66682170-66683128	PBDE	blood:	n/a	n/a
2	POLR2A	chr11:66682729-66682860	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:66682806-66682938	K562	blood:	n/a	n/a
4	POLR2A	chr11:66682582-66683125	H1-neurons	neurons:	n/a	n/a
5	TAL1	chr11:66682664-66682894	K562	blood:	n/a	chr11:66682751-66682769
6	CTCF	chr11:66682860-66683010	A549	lung:	n/a	n/a
7	GATA1	chr11:66682387-66683276	PBDE	blood:	n/a	chr11:66682760-66682769 chr11:66682751-66682768

No.	Distal block	Cell Line	Cell type
1	chr11:66681518..66683376-chr11:66724047..66725843,2	MCF-7	breast:
2	chr11:66671241..66674201-chr11:66681070..66683415,2	MCF-7	breast:
3	chr11:66681279..66683379-chr11:66773708..66775919,2	MCF-7	breast:
4	chr11:66644476..66647274-chr11:66681584..66683637,2	MCF-7	breast:

Variant related genes	Relation type
RNU7-23P	TF binding region
ENSG00000173227	Chromatin interaction
ENSG00000173599	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1077256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791894	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791896	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227625	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs11227628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227630	0.86[ASN][1000 genomes]
rs1530891	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1901376	0.91[ASN][1000 genomes]
rs34482178	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4483596	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4930393	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930394	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591226	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67156018	0.89[ASN][1000 genomes]
rs7107498	0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7110302	0.87[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs7119682	0.87[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs746018	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746019	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935749	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936290	0.86[ASN][1000 genomes]
rs7944999	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7952017	0.91[ASN][1000 genomes]
rs966021	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[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	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11227624	B3GNT1	cis	parietal	SCAN
rs11227624	ACTN3	cis	Muscle Skeletal	GTEx
rs11227624	SLC25A45	cis	parietal	SCAN
rs11227624	PC	cis	cerebellum	SCAN
rs11227624	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs11227624	EHBP1L1	cis	cerebellum	SCAN
rs11227624	FGF4	cis	parietal	SCAN
rs11227624	CDC42BPG	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66672200-66684000	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr11:66672600-66683000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:66674000-66687000	Weak transcription	HSMMtube	muscle
4	chr11:66674400-66689600	Weak transcription	NHLF	lung
5	chr11:66674600-66684800	Weak transcription	Fetal Stomach	stomach
6	chr11:66674600-66696400	Weak transcription	NHEK	skin
7	chr11:66675000-66696200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:66675600-66683000	Weak transcription	A549	lung
9	chr11:66675600-66687000	Weak transcription	Osteobl	bone
10	chr11:66675600-66699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:66676200-66688600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:66676800-66683800	Weak transcription	Fetal Brain Female	brain
13	chr11:66676800-66696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:66677000-66683000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr11:66677200-66683400	Weak transcription	Liver	Liver
16	chr11:66677200-66692000	Weak transcription	Pancreas	Pancrea
17	chr11:66678000-66688600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:66678400-66683600	Weak transcription	Hela-S3	cervix
19	chr11:66680200-66686800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:66680600-66683000	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:66680600-66683600	Enhancers	HepG2	liver
22	chr11:66680600-66684000	Enhancers	Brain Anterior Caudate	brain
23	chr11:66680600-66684200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:66680600-66684200	Enhancers	Brain Substantia Nigra	brain
25	chr11:66680600-66684600	Weak transcription	Right Ventricle	heart
26	chr11:66680600-66689000	Weak transcription	Brain Germinal Matrix	brain
27	chr11:66680800-66683000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:66680800-66683000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:66680800-66687000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:66682000-66684000	Enhancers	Stomach Mucosa	stomach
31	chr11:66682000-66684000	Enhancers	K562	blood
32	chr11:66682200-66683200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr11:66682200-66683800	Strong transcription	Fetal Intestine Small	intestine
34	chr11:66682200-66684200	Enhancers	Brain Angular Gyrus	brain
35	chr11:66682400-66683400	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr11:66682400-66683800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr11:66682400-66683800	Enhancers	Gastric	stomach
38	chr11:66682400-66685400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:66682600-66683000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:66682600-66683000	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr11:66682600-66683400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr11:66682600-66683400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr11:66682600-66683600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:66682600-66683600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr11:66682600-66683600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr11:66682600-66683800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:66682600-66683800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:66682600-66684000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:66682600-66684000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr11:66682600-66684200	Enhancers	Rectal Mucosa Donor 31	rectum

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