Variant report

Variant	rs10082834
Chromosome Location	chr12:12334006-12334007
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12333575..12335738-chr12:12341960..12344629,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10083170	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10466847	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466848	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845497	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845499	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10845500	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054695	1.00[ASN][1000 genomes]
rs11054696	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054706	1.00[ASN][1000 genomes]
rs11054707	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054720	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11054729	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11054732	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054767	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1123213	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831610	1.00[ASN][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297598	0.85[EUR][1000 genomes]
rs12304957	0.81[EUR][1000 genomes]
rs12305378	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306293	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306537	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309246	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309338	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12309495	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12310020	1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12311202	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319942	0.85[EUR][1000 genomes]
rs12422890	1.00[ASN][1000 genomes]
rs12424332	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424361	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425699	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427198	0.82[EUR][1000 genomes]
rs13377971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907789	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907821	1.00[YRI][hapmap]
rs28448423	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56259928	1.00[ASN][1000 genomes]
rs56998126	0.85[EUR][1000 genomes]
rs57055264	0.94[EUR][1000 genomes]
rs58682800	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59386755	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7311064	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061123	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74061145	0.85[EUR][1000 genomes]
rs7957531	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7960716	0.85[EUR][1000 genomes]
rs7973718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7978064	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs7979919	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630249	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630250	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[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	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
rs10082834	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 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	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:12312200-12334600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
13	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
15	chr12:12312800-12337600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:12314000-12335600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:12314000-12336000	Weak transcription	Adipose Nuclei	Adipose
18	chr12:12314400-12336000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:12315400-12340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:12315400-12371600	Weak transcription	Lung	lung
21	chr12:12317600-12335600	Weak transcription	Fetal Stomach	stomach
22	chr12:12317800-12335400	Weak transcription	Fetal Kidney	kidney
23	chr12:12318200-12335600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:12318200-12335600	Weak transcription	Left Ventricle	heart
25	chr12:12318200-12335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:12322000-12334200	Weak transcription	Gastric	stomach
27	chr12:12325400-12335800	Weak transcription	Osteobl	bone
28	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:12325600-12335000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:12325800-12334200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:12325800-12335600	Weak transcription	Fetal Brain Female	brain
32	chr12:12325800-12335600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:12325800-12341000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:12326200-12334400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:12327800-12334200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:12328200-12335600	Weak transcription	Stomach Mucosa	stomach
37	chr12:12328400-12335600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:12328400-12339800	Weak transcription	Ovary	ovary
39	chr12:12328600-12339000	Weak transcription	Fetal Intestine Small	intestine
40	chr12:12329000-12334800	Strong transcription	Liver	Liver
41	chr12:12329600-12343200	Weak transcription	Placenta	Placenta
42	chr12:12330200-12343200	Weak transcription	GM12878-XiMat	blood
43	chr12:12330400-12334400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:12330400-12334800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:12330600-12335800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:12330600-12336000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:12330800-12334200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:12330800-12334400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:12331000-12334600	Weak transcription	Colonic Mucosa	Colon
50	chr12:12331000-12335400	Weak transcription	Fetal Brain Male	brain

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