Variant report

Variant	rs10845488
Chromosome Location	chr12:12311367-12311368
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12311196..12313408-chr12:12319093..12320757,2	K562	blood:
2	chr12:12310500..12312178-chr12:12419652..12422450,2	K562	blood:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10400407	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10466849	0.88[CEU][hapmap]
rs11054703	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12313200	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12314259	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12320259	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12422312	0.87[CEU][hapmap]
rs12425946	0.87[CEU][hapmap]
rs34143386	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6488506	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs718403	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7301012	0.93[CEU][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7308712	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7963810	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][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
rs10845488	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
3	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
6	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
8	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:12279800-12311600	Weak transcription	Dnd41	blood
10	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
13	chr12:12285000-12311400	Weak transcription	Pancreas	Pancrea
14	chr12:12285600-12315000	Weak transcription	Fetal Heart	heart
15	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:12288200-12342800	Weak transcription	K562	blood
17	chr12:12288600-12311400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:12297600-12321400	Weak transcription	Gastric	stomach
21	chr12:12298800-12312200	Strong transcription	Fetal Intestine Large	intestine
22	chr12:12300600-12315800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:12300800-12313200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:12302000-12311400	Weak transcription	Aorta	Aorta
25	chr12:12302000-12311800	Weak transcription	Lung	lung
26	chr12:12302000-12318000	Weak transcription	Stomach Mucosa	stomach
27	chr12:12302200-12325000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:12302400-12313000	Weak transcription	NHLF	lung
30	chr12:12302600-12311400	Weak transcription	Brain Angular Gyrus	brain
31	chr12:12302800-12311400	Weak transcription	Fetal Brain Female	brain
32	chr12:12302800-12317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:12303600-12318200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:12303800-12316200	Weak transcription	GM12878-XiMat	blood
35	chr12:12303800-12316600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:12303800-12335600	Weak transcription	Right Ventricle	heart
37	chr12:12304000-12311600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:12304000-12311800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:12304000-12311800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:12304000-12312400	Weak transcription	HUVEC	blood vessel
41	chr12:12304000-12312600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:12304000-12313000	Weak transcription	NHEK	skin
43	chr12:12304000-12313400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:12304000-12315000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:12304000-12315000	Weak transcription	Brain Substantia Nigra	brain
46	chr12:12304000-12319800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:12304200-12311400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:12304200-12311600	Weak transcription	HSMMtube	muscle
50	chr12:12304200-12313600	Weak transcription	Rectal Mucosa Donor 31	rectum

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