Variant report

Variant	rs7973718
Chromosome Location	chr12:12342821-12342822
allele	A/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: 56 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10083170	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	1.00[CHB][hapmap]
rs10845497	0.90[EUR][1000 genomes]
rs10845499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.85[EUR][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054707	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11054720	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]
rs11054729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs11054767	1.00[JPT][hapmap]
rs1123213	0.81[EUR][1000 genomes]
rs11829211	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12297598	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12309246	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12309338	1.00[JPT][hapmap]
rs12310020	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12311922	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12319942	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	1.00[CHB][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap]
rs12425185	0.89[EUR][1000 genomes]
rs12425699	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12425946	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs12427198	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16907789	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs28448423	0.90[EUR][1000 genomes]
rs56998126	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74061123	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.81[AFR][1000 genomes];0.89[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];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9630266	1.00[CEU][hapmap];1.00[JPT][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
rs7973718	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
3	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
7	chr12:12315400-12371600	Weak transcription	Lung	lung
8	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:12329600-12343200	Weak transcription	Placenta	Placenta
10	chr12:12330200-12343200	Weak transcription	GM12878-XiMat	blood
11	chr12:12334200-12350800	Weak transcription	Fetal Thymus	thymus
12	chr12:12334400-12343200	Weak transcription	Fetal Intestine Large	intestine
13	chr12:12334400-12348400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:12334400-12349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:12334400-12349600	Weak transcription	Dnd41	blood
16	chr12:12334400-12351200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:12334600-12349200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:12334800-12346800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:12335200-12352000	Weak transcription	HSMM	muscle
24	chr12:12335200-12365800	Weak transcription	NHEK	skin
25	chr12:12335800-12343600	Weak transcription	HMEC	breast
26	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
27	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:12336000-12354200	Weak transcription	Primary T cells from cord blood	blood
29	chr12:12336000-12355600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:12336200-12343000	Weak transcription	Brain Substantia Nigra	brain
31	chr12:12336200-12343200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:12336200-12343400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:12336200-12343600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:12336200-12347000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:12336200-12360000	Weak transcription	Aorta	Aorta
36	chr12:12336200-12363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
38	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
39	chr12:12336400-12343400	Weak transcription	Brain Angular Gyrus	brain
40	chr12:12336400-12343800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:12336400-12343800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:12336400-12343800	Weak transcription	HUVEC	blood vessel
43	chr12:12336400-12344000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:12336400-12344000	Weak transcription	Brain Anterior Caudate	brain
45	chr12:12336400-12348800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:12336400-12349600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:12336400-12357400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:12336600-12343200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:12336600-12343600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:12336600-12343600	Weak transcription	NH-A	brain

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