Variant report

Variant	rs12425946
Chromosome Location	chr12:12410964-12410965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12410046..12415348-chr12:12416072..12422539,9	MCF-7	breast:
2	chr12:12401717..12403470-chr12:12410305..12412865,2	MCF-7	breast:
3	chr12:12409427..12413738-chr12:12419766..12421892,3	K562	blood:
4	chr12:12410568..12413506-chr12:12416541..12418558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction
ENSG00000270857	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10466849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845488	0.87[CEU][hapmap]
rs10845499	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs11054720	1.00[CHB][hapmap]
rs11054729	1.00[CHB][hapmap]
rs11054732	1.00[CHB][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap]
rs11054765	1.00[CHB][hapmap]
rs11834671	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299540	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313200	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs12317629	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12320259	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs12321417	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56087862	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488506	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs718403	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7301012	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs7308022	1.00[CHB][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap]
rs74061128	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061161	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	1.00[CHB][hapmap]
rs7963810	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7973718	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs7978064	1.00[CHB][hapmap];0.81[LWK][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	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
rs12425946	LRP6	Cis_1M	lymphoblastoid	RTeQTL
rs12425946	RIMKLB	cis	cerebellum	SCAN

Chromatin state (count:45 , 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	chr12:12406000-12412600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:12406200-12411800	Weak transcription	Fetal Intestine Small	intestine
20	chr12:12406400-12416800	Weak transcription	Hela-S3	cervix
21	chr12:12407400-12416600	Weak transcription	Fetal Brain Male	brain
22	chr12:12408200-12416800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:12408400-12416800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:12408400-12417200	Weak transcription	NHLF	lung
25	chr12:12408400-12417400	Weak transcription	NH-A	brain
26	chr12:12408400-12417400	Weak transcription	NHDF-Ad	bronchial
27	chr12:12408400-12418200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:12408600-12417800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:12408800-12417200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:12409000-12413400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:12409000-12416600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:12409000-12417400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:12409400-12417200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:12409600-12416600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:12409600-12416600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:12409600-12416600	Weak transcription	Ovary	ovary
37	chr12:12409800-12411000	Weak transcription	Pancreas	Pancrea
38	chr12:12409800-12411600	Weak transcription	Right Atrium	heart
39	chr12:12410000-12414400	Weak transcription	Liver	Liver
40	chr12:12410000-12416800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:12410200-12411200	Weak transcription	A549	lung
42	chr12:12410200-12415400	Weak transcription	HepG2	liver
43	chr12:12410200-12416800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:12410200-12417000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:12410200-12417200	Weak transcription	Osteobl	bone

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