Variant report

Variant	rs746019
Chromosome Location	chr11:66677336-66677337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66677241..66680010-chr11:66694798..66696500,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1077256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791894	0.94[ASW][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791896	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227624	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]
rs11227625	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]
rs11227628	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227630	0.86[ASN][1000 genomes]
rs1530891	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1901376	0.91[ASN][1000 genomes]
rs34482178	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4483596	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930393	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930394	0.94[ASW][hapmap];1.00[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591226	0.94[ASW][hapmap];1.00[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];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67156018	0.89[ASN][1000 genomes]
rs7107498	0.87[CHB][hapmap];0.86[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	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs746018	0.94[ASW][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935749	0.94[ASW][hapmap];1.00[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];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936290	0.86[ASN][1000 genomes]
rs7944999	0.85[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	0.85[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs746019	PC	cis	cerebellum	SCAN
rs746019	B3GNT1	cis	parietal	SCAN
rs746019	ACTN3	cis	Muscle Skeletal	GTEx
rs746019	CDC42BPG	cis	cerebellum	SCAN
rs746019	FGF4	cis	parietal	SCAN
rs746019	CCS	cis	multi-tissue	Pritchard
rs746019	LRFN4	cis	multi-tissue	Pritchard
rs746019	SLC25A45	cis	parietal	SCAN
rs746019	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs746019	EHBP1L1	cis	cerebellum	SCAN
rs746019	SUV420H1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66651400-66678400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:66672200-66684000	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr11:66672600-66680000	Weak transcription	HUVEC	blood vessel
4	chr11:66672600-66683000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:66673600-66678000	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr11:66674000-66687000	Weak transcription	HSMMtube	muscle
7	chr11:66674200-66677800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:66674200-66679600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:66674200-66680000	Weak transcription	Brain Germinal Matrix	brain
10	chr11:66674400-66677800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:66674400-66677800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr11:66674400-66679400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:66674400-66679600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:66674400-66679600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:66674400-66679600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:66674400-66679800	Weak transcription	Brain Anterior Caudate	brain
17	chr11:66674400-66689600	Weak transcription	NHLF	lung
18	chr11:66674600-66678000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr11:66674600-66679600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:66674600-66679800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:66674600-66680000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:66674600-66680400	Weak transcription	Right Ventricle	heart
23	chr11:66674600-66684800	Weak transcription	Fetal Stomach	stomach
24	chr11:66674600-66696400	Weak transcription	NHEK	skin
25	chr11:66674800-66679800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:66674800-66680200	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:66675000-66696200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:66675400-66679800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:66675400-66680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:66675400-66681400	Weak transcription	Fetal Intestine Large	intestine
31	chr11:66675600-66682000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:66675600-66683000	Weak transcription	A549	lung
33	chr11:66675600-66687000	Weak transcription	Osteobl	bone
34	chr11:66675600-66699800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:66675800-66678000	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:66675800-66679600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr11:66675800-66680000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:66675800-66680400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:66675800-66682200	Weak transcription	Fetal Intestine Small	intestine
40	chr11:66676000-66677400	Genic enhancers	Hela-S3	cervix
41	chr11:66676000-66678200	Weak transcription	Fetal Kidney	kidney
42	chr11:66676000-66679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:66676000-66679800	Weak transcription	Brain Angular Gyrus	brain
44	chr11:66676000-66680000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:66676000-66680000	Weak transcription	Stomach Mucosa	stomach
46	chr11:66676200-66678000	Weak transcription	Psoas Muscle	Psoas
47	chr11:66676200-66678800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:66676200-66682000	Weak transcription	K562	blood
49	chr11:66676200-66682400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:66676200-66688600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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