Variant report

Variant	rs11054720
Chromosome Location	chr12:12330894-12330895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12329160..12332545-chr12:12419382..12422512,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10083170	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466847	0.81[EUR][1000 genomes]
rs10466849	1.00[CHB][hapmap]
rs10845497	0.87[EUR][1000 genomes]
rs10845499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.85[EUR][1000 genomes]
rs11054702	1.00[CEU][hapmap]
rs11054705	1.00[CEU][hapmap]
rs11054707	1.00[CEU][hapmap]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs11054767	1.00[JPT][hapmap]
rs1123213	0.84[EUR][1000 genomes]
rs11829211	0.92[EUR][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12297598	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12309246	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12310020	1.00[JPT][hapmap]
rs12311922	0.87[EUR][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12319942	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	1.00[CHB][hapmap]
rs12425185	0.89[EUR][1000 genomes]
rs12425699	1.00[CEU][hapmap]
rs12425946	1.00[CHB][hapmap]
rs12427198	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap]
rs16907789	1.00[CEU][hapmap]
rs28448423	0.87[EUR][1000 genomes]
rs56998126	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.89[EUR][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.87[EUR][1000 genomes]
rs74061123	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.85[EUR][1000 genomes]
rs9630266	1.00[CEU][hapmap]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11054720	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
4	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
6	chr12:12288200-12342800	Weak transcription	K562	blood
7	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
9	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:12312000-12332600	Weak transcription	Dnd41	blood
11	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:12312200-12334000	Weak transcription	Pancreas	Pancrea
13	chr12:12312200-12334600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
17	chr12:12312400-12332400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:12312400-12332600	Weak transcription	Fetal Thymus	thymus
19	chr12:12312800-12337600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:12314000-12331400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:12314000-12333200	Weak transcription	NH-A	brain
22	chr12:12314000-12335600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:12314000-12336000	Weak transcription	Adipose Nuclei	Adipose
24	chr12:12314400-12336000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:12315400-12334000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:12315400-12340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:12315400-12371600	Weak transcription	Lung	lung
28	chr12:12316200-12332400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:12317400-12332400	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:12317600-12331400	Weak transcription	HUVEC	blood vessel
31	chr12:12317600-12331600	Weak transcription	Fetal Intestine Large	intestine
32	chr12:12317600-12332800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:12317600-12335600	Weak transcription	Fetal Stomach	stomach
34	chr12:12317800-12335400	Weak transcription	Fetal Kidney	kidney
35	chr12:12318200-12331400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:12318200-12335600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:12318200-12335600	Weak transcription	Left Ventricle	heart
38	chr12:12318200-12335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:12318400-12334000	Weak transcription	Brain Substantia Nigra	brain
40	chr12:12322000-12334200	Weak transcription	Gastric	stomach
41	chr12:12325400-12331400	Weak transcription	Brain Anterior Caudate	brain
42	chr12:12325400-12331600	Weak transcription	Brain Angular Gyrus	brain
43	chr12:12325400-12334000	Weak transcription	NHLF	lung
44	chr12:12325400-12335800	Weak transcription	Osteobl	bone
45	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:12325600-12331600	Weak transcription	Fetal Lung	lung
47	chr12:12325600-12332000	Weak transcription	Primary T cells from cord blood	blood
48	chr12:12325600-12332200	Weak transcription	HepG2	liver
49	chr12:12325600-12332600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:12325600-12335000	Weak transcription	Brain Cingulate Gyrus	brain

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