Variant report

Variant	rs2160525
Chromosome Location	chr12:12270290-12270291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MANSC1-2	chr12:12268963-12272807	NONHSAT026963

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10466846	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10772533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11054704	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11054741	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs1181332	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs12314349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12823867	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs2302685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7980903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2160525	PRH1	cis	parietal	SCAN
rs2160525	LRP6	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr12:12241000-12273400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:12241400-12272600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:12246400-12272000	Weak transcription	Osteobl	bone
5	chr12:12248200-12271800	Weak transcription	Fetal Kidney	kidney
6	chr12:12252800-12276200	Weak transcription	Fetal Heart	heart
7	chr12:12258200-12274000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:12260800-12273400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr12:12260800-12276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:12260800-12277000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:12261000-12271400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:12261000-12276800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:12261200-12273000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:12261200-12273400	Weak transcription	HSMMtube	muscle
15	chr12:12261200-12274000	Weak transcription	Ovary	ovary
16	chr12:12261200-12277000	Weak transcription	Hela-S3	cervix
17	chr12:12261400-12275800	Weak transcription	NH-A	brain
18	chr12:12261600-12301400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:12261800-12271600	Weak transcription	Primary T cells from cord blood	blood
20	chr12:12261800-12271600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr12:12261800-12288000	Weak transcription	Gastric	stomach
22	chr12:12262200-12271200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:12262200-12277200	Weak transcription	Brain Germinal Matrix	brain
24	chr12:12262400-12271800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:12262400-12277200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:12262600-12272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:12262800-12272600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:12262800-12273000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:12262800-12273400	Weak transcription	Left Ventricle	heart
31	chr12:12262800-12284800	Weak transcription	Aorta	Aorta
32	chr12:12263200-12271800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr12:12263600-12272000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
35	chr12:12264000-12271800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:12264000-12272000	Weak transcription	Adipose Nuclei	Adipose
37	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
38	chr12:12264200-12284600	Weak transcription	Pancreas	Pancrea
39	chr12:12264400-12273000	Weak transcription	Placenta	Placenta
40	chr12:12264400-12273200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:12264400-12273400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:12264400-12284800	Weak transcription	Lung	lung
43	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:12264600-12272200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:12264600-12273200	Weak transcription	Fetal Intestine Large	intestine
46	chr12:12264600-12276400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:12265000-12271000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:12265400-12279000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:12266000-12274000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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