Variant report

Variant	rs10845501
Chromosome Location	chr12:12415697-12415698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10431302	0.85[ASW][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs10431304	0.82[EUR][1000 genomes]
rs10492120	0.90[CHB][hapmap]
rs10743980	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10772536	0.88[EUR][1000 genomes]
rs10772537	0.86[EUR][1000 genomes]
rs10772540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10772542	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs10772546	0.82[EUR][1000 genomes]
rs10772547	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs10845489	0.93[CEU][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs10845491	0.80[EUR][1000 genomes]
rs10845492	0.87[EUR][1000 genomes]
rs10845494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10845495	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054721	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[YRI][hapmap]
rs11054724	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11054731	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054744	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11054754	0.85[EUR][1000 genomes]
rs11609634	0.93[CEU][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs12366664	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12823243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17819999	0.92[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1819871	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2284396	0.93[CEU][hapmap];0.83[MEX][hapmap]
rs2417085	1.00[CHB][hapmap]
rs2417086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3782528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4477532	0.93[CEU][hapmap];0.87[MEX][hapmap]
rs4763785	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4763794	0.86[TSI][hapmap]
rs4763795	0.82[TSI][hapmap]
rs61920859	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488507	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7294695	0.93[CEU][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes]
rs7301935	0.89[ASN][1000 genomes]
rs7302808	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7305037	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7956548	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7956971	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966410	0.92[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7973531	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs7975772	0.82[EUR][1000 genomes]
rs7979447	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9300240	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10845501	LRP6	cis	parietal	SCAN
rs10845501	AICDA	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:12384800-12417200	Weak transcription	K562	blood
3	chr12:12385000-12417800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:12390000-12416600	Weak transcription	Psoas Muscle	Psoas
5	chr12:12390800-12417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:12394200-12416800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:12394200-12417400	Weak transcription	Fetal Kidney	kidney
8	chr12:12394800-12417400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:12395600-12417400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:12397600-12416600	Weak transcription	Fetal Stomach	stomach
11	chr12:12397800-12416800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:12397800-12417200	Weak transcription	Brain Anterior Caudate	brain
13	chr12:12401200-12418000	Weak transcription	Brain Substantia Nigra	brain
14	chr12:12402400-12417200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:12405000-12416600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:12405200-12416600	Weak transcription	Left Ventricle	heart
17	chr12:12405600-12417400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:12406400-12416800	Weak transcription	Hela-S3	cervix
19	chr12:12407400-12416600	Weak transcription	Fetal Brain Male	brain
20	chr12:12408200-12416800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:12408400-12416800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr12:12408400-12417200	Weak transcription	NHLF	lung
23	chr12:12408400-12417400	Weak transcription	NH-A	brain
24	chr12:12408400-12417400	Weak transcription	NHDF-Ad	bronchial
25	chr12:12408400-12418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:12408600-12417800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:12408800-12417200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:12409000-12416600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:12409000-12417400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:12409400-12417200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:12409600-12416600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:12409600-12416600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:12409600-12416600	Weak transcription	Ovary	ovary
34	chr12:12410000-12416800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:12410200-12416800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:12410200-12417000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:12410200-12417200	Weak transcription	Osteobl	bone
38	chr12:12413400-12416000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:12413400-12417400	Weak transcription	Fetal Intestine Small	intestine
40	chr12:12413800-12415800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:12413800-12416800	Weak transcription	GM12878-XiMat	blood
42	chr12:12414400-12416600	Enhancers	Liver	Liver
43	chr12:12414400-12416800	Weak transcription	Right Atrium	heart
44	chr12:12414800-12416400	Weak transcription	A549	lung
45	chr12:12415400-12415800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:12415400-12416600	Weak transcription	Pancreas	Pancrea
47	chr12:12415600-12416400	Weak transcription	HepG2	liver

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