Variant report

Variant	rs897057
Chromosome Location	chr12:50266279-50266280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50262446..50266372-chr12:50284381..50286469,3	MCF-7	breast:
2	chr12:50266064..50268660-chr12:50284486..50286265,2	K562	blood:
3	chr12:50236583..50238267-chr12:50264548..50267358,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186666	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1044677	0.91[TSI][hapmap]
rs10747567	0.84[EUR][1000 genomes]
rs10747568	0.84[EUR][1000 genomes]
rs10783321	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs10783323	0.84[EUR][1000 genomes]
rs10783326	0.84[EUR][1000 genomes]
rs10875984	0.81[EUR][1000 genomes]
rs1248263	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1248264	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1563168	0.83[EUR][1000 genomes]
rs1869504	0.81[EUR][1000 genomes]
rs1965873	0.82[EUR][1000 genomes]
rs2271687	0.84[EUR][1000 genomes]
rs2271688	0.84[EUR][1000 genomes]
rs3741557	0.84[EUR][1000 genomes]
rs3741558	0.83[EUR][1000 genomes]
rs383307	0.81[CHD][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs423934	0.84[CHD][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs4391887	0.80[TSI][hapmap]
rs4898512	0.82[EUR][1000 genomes]
rs4898513	0.82[EUR][1000 genomes]
rs4898536	0.87[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4898537	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4898539	0.87[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs67723963	0.81[EUR][1000 genomes]
rs706797	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137210	0.83[EUR][1000 genomes]
rs7295882	0.84[EUR][1000 genomes]
rs7302465	0.81[EUR][1000 genomes]
rs7306374	0.84[EUR][1000 genomes]
rs7954572	0.87[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7967564	0.83[EUR][1000 genomes]
rs7969178	0.84[EUR][1000 genomes]
rs836959	0.84[CHD][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.83[ASN][1000 genomes]
rs836967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836969	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836970	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9805137	0.84[EUR][1000 genomes]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs897057	FAM186B	cis	cerebellum	SCAN
rs897057	BCDIN3D	cis	parietal	SCAN
rs897057	C12orf62	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50260600-50267600	Enhancers	HSMM	muscle
2	chr12:50260600-50268200	Enhancers	HSMMtube	muscle
3	chr12:50260600-50268600	Enhancers	Fetal Muscle Leg	muscle
4	chr12:50261000-50268200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:50261200-50267000	Enhancers	Right Atrium	heart
6	chr12:50262000-50270800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:50263400-50267000	Weak transcription	Fetal Kidney	kidney
8	chr12:50263600-50270800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:50263800-50266400	Enhancers	Brain Germinal Matrix	brain
10	chr12:50263800-50266400	Weak transcription	NHDF-Ad	bronchial
11	chr12:50263800-50266600	Weak transcription	Lung	lung
12	chr12:50263800-50266600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:50263800-50266600	Weak transcription	Osteobl	bone
14	chr12:50263800-50268000	Weak transcription	Gastric	stomach
15	chr12:50263800-50268400	Weak transcription	Esophagus	oesophagus
16	chr12:50263800-50271800	Weak transcription	Pancreas	Pancrea
17	chr12:50264000-50267200	Weak transcription	Fetal Intestine Small	intestine
18	chr12:50264000-50268800	Enhancers	Hela-S3	cervix
19	chr12:50264600-50271600	Weak transcription	Fetal Brain Male	brain
20	chr12:50264800-50269200	Enhancers	Brain Substantia Nigra	brain
21	chr12:50265000-50266800	Enhancers	Brain Angular Gyrus	brain
22	chr12:50265200-50266600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:50265200-50266600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:50265200-50267400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:50265200-50268000	Weak transcription	Right Ventricle	heart
26	chr12:50265200-50268200	Enhancers	Fetal Muscle Trunk	muscle
27	chr12:50265200-50268400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr12:50265200-50269200	Enhancers	Brain Hippocampus Middle	brain
29	chr12:50265600-50266400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:50265800-50266400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:50265800-50266400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:50265800-50266600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:50265800-50266600	Enhancers	NH-A	brain
34	chr12:50265800-50267000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr12:50265800-50267200	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr12:50265800-50268200	Genic enhancers	Brain Anterior Caudate	brain
37	chr12:50265800-50269200	Enhancers	Placenta	Placenta
38	chr12:50266000-50266400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr12:50266000-50266600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:50266000-50266800	Enhancers	K562	blood
41	chr12:50266000-50267200	Enhancers	Fetal Heart	heart
42	chr12:50266000-50267400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:50266000-50267600	Enhancers	Left Ventricle	heart
44	chr12:50266000-50268000	Enhancers	Adipose Nuclei	Adipose
45	chr12:50266000-50268400	Enhancers	Fetal Stomach	stomach
46	chr12:50266000-50268600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr12:50266200-50266400	Enhancers	Fetal Thymus	thymus
48	chr12:50266200-50266600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:50266200-50266600	Weak transcription	Fetal Brain Female	brain
50	chr12:50266200-50267800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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