Variant report

Variant	rs7978064
Chromosome Location	chr12:12336966-12336967
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	chr12:12315377..12318046-chr12:12335015..12337960,2	K562	blood:
2	chr12:12336035..12338491-chr12:12459842..12461495,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10082834	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs10083170	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	1.00[CHB][hapmap]
rs10845497	0.85[EUR][1000 genomes]
rs10845499	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.83[EUR][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054707	0.82[CEU][hapmap]
rs11054709	0.82[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs11054710	0.82[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs11054713	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs11054720	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	0.82[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.85[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs1123213	0.86[EUR][1000 genomes]
rs11829211	0.94[EUR][1000 genomes]
rs12296239	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs12297598	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	0.82[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12309246	0.82[CEU][hapmap]
rs12310020	0.81[MEX][hapmap]
rs12311922	0.85[EUR][1000 genomes]
rs12316043	0.82[CEU][hapmap];0.87[MEX][hapmap]
rs12319942	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	1.00[CHB][hapmap]
rs12425185	0.87[EUR][1000 genomes]
rs12425699	0.82[CEU][hapmap]
rs12425946	1.00[CHB][hapmap];0.81[LWK][hapmap]
rs12427198	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	0.82[CEU][hapmap]
rs16907789	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs28448423	0.85[EUR][1000 genomes]
rs56998126	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.90[EUR][1000 genomes]
rs7308022	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74061123	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061128	0.83[AFR][1000 genomes]
rs74061145	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	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	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9630266	0.82[CEU][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
rs7978064	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:12288200-12342800	Weak transcription	K562	blood
5	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:12304000-12353000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:12312000-12350600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:12312200-12338000	Weak transcription	Brain Germinal Matrix	brain
9	chr12:12312200-12355800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:12312200-12362000	Weak transcription	Hela-S3	cervix
11	chr12:12312800-12337600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:12315400-12340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:12315400-12371600	Weak transcription	Lung	lung
14	chr12:12325400-12360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:12325800-12341000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:12328400-12339800	Weak transcription	Ovary	ovary
17	chr12:12328600-12339000	Weak transcription	Fetal Intestine Small	intestine
18	chr12:12329600-12343200	Weak transcription	Placenta	Placenta
19	chr12:12330200-12343200	Weak transcription	GM12878-XiMat	blood
20	chr12:12332600-12337400	Genic enhancers	A549	lung
21	chr12:12334000-12338600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:12334200-12337000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:12334200-12350800	Weak transcription	Fetal Thymus	thymus
24	chr12:12334400-12338800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:12334400-12339200	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:12334400-12339800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:12334400-12343200	Weak transcription	Fetal Intestine Large	intestine
28	chr12:12334400-12348400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:12334400-12349200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:12334400-12349600	Weak transcription	Dnd41	blood
31	chr12:12334400-12351200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:12334400-12352000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:12334400-12354000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:12334400-12367600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:12334600-12337600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:12334600-12349200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:12334800-12337000	Enhancers	Brain Hippocampus Middle	brain
38	chr12:12334800-12346800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:12334800-12352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:12335200-12352000	Weak transcription	HSMM	muscle
41	chr12:12335200-12365800	Weak transcription	NHEK	skin
42	chr12:12335400-12337000	Enhancers	Fetal Brain Male	brain
43	chr12:12335600-12337000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:12335600-12337000	Enhancers	Small Intestine	intestine
45	chr12:12335600-12337400	Enhancers	Rectal Smooth Muscle	rectum
46	chr12:12335600-12338400	Enhancers	Fetal Brain Female	brain
47	chr12:12335800-12343600	Weak transcription	HMEC	breast
48	chr12:12335800-12354000	Weak transcription	HSMMtube	muscle
49	chr12:12336000-12338000	Genic enhancers	HepG2	liver
50	chr12:12336000-12352000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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