Variant report

Variant	rs11227625
Chromosome Location	chr11:66684151-66684152
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66679281..66682230-chr11:66683799..66685977,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1077256	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10791894	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs10791896	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227624	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227630	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1530891	0.80[CEU][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap]
rs1901376	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930394	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs6591226	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs67156018	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107498	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7110302	0.91[JPT][hapmap]
rs7119682	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs746018	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs746019	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7935749	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7936290	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7944999	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952017	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966021	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11227625	RPS6KA4	cis	cerebellum	SCAN
rs11227625	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs11227625	B3GNT1	cis	parietal	SCAN
rs11227625	FGF4	cis	parietal	SCAN
rs11227625	CDC42BPG	cis	cerebellum	SCAN
rs11227625	NXF1	cis	parietal	SCAN
rs11227625	EHBP1L1	cis	cerebellum	SCAN
rs11227625	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs11227625	SLC25A45	cis	parietal	SCAN
rs11227625	PC	cis	cerebellum	SCAN
rs11227625	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66674000-66687000	Weak transcription	HSMMtube	muscle
2	chr11:66674400-66689600	Weak transcription	NHLF	lung
3	chr11:66674600-66684800	Weak transcription	Fetal Stomach	stomach
4	chr11:66674600-66696400	Weak transcription	NHEK	skin
5	chr11:66675000-66696200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:66675600-66687000	Weak transcription	Osteobl	bone
7	chr11:66675600-66699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:66676200-66688600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:66676800-66696400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:66677200-66692000	Weak transcription	Pancreas	Pancrea
11	chr11:66678000-66688600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:66680200-66686800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:66680600-66684200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:66680600-66684200	Enhancers	Brain Substantia Nigra	brain
15	chr11:66680600-66684600	Weak transcription	Right Ventricle	heart
16	chr11:66680600-66689000	Weak transcription	Brain Germinal Matrix	brain
17	chr11:66680800-66687000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:66682200-66684200	Enhancers	Brain Angular Gyrus	brain
19	chr11:66682400-66685400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:66682600-66684200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr11:66682600-66684600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:66682600-66685400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr11:66682600-66687400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:66682800-66684200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:66683000-66684400	Enhancers	Brain Cingulate Gyrus	brain
26	chr11:66683000-66684800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:66683000-66685200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:66683000-66685600	Enhancers	A549	lung
29	chr11:66683200-66688600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:66683200-66698200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr11:66683400-66688600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr11:66683400-66688600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:66683600-66687200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:66683600-66687400	Weak transcription	Adipose Nuclei	Adipose
35	chr11:66683600-66687600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:66683600-66688400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:66683600-66688600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:66683800-66686000	Weak transcription	Gastric	stomach
39	chr11:66683800-66687000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:66683800-66687200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:66683800-66687400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:66683800-66687400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr11:66683800-66692400	Weak transcription	Fetal Intestine Small	intestine
44	chr11:66684000-66685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:66684000-66685200	Weak transcription	Liver	Liver
46	chr11:66684000-66685600	Weak transcription	Stomach Mucosa	stomach
47	chr11:66684000-66686000	Weak transcription	Hela-S3	cervix
48	chr11:66684000-66686000	Weak transcription	K562	blood
49	chr11:66684000-66687000	Weak transcription	Brain Anterior Caudate	brain
50	chr11:66684000-66687000	Weak transcription	Brain Hippocampus Middle	brain

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